From 62f673ff2d480e0c84b676ed0c6f4fbdfb5eec43 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Sun, 11 Oct 2026 18:51:10 -0700 Subject: [PATCH 1/4] Claim PAYTON2017_HAB_AMINUTUM (PRJEB18614) --- config/PAYTON2017_HAB_AMINUTUM.config | 23 +++++++ registry/studies/PAYTON2017_HAB_AMINUTUM.yaml | 62 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 config/PAYTON2017_HAB_AMINUTUM.config create mode 100644 registry/studies/PAYTON2017_HAB_AMINUTUM.yaml diff --git a/config/PAYTON2017_HAB_AMINUTUM.config b/config/PAYTON2017_HAB_AMINUTUM.config new file mode 100644 index 0000000..deefa91 --- /dev/null +++ b/config/PAYTON2017_HAB_AMINUTUM.config @@ -0,0 +1,23 @@ +/* + * AREE :: run configuration for PAYTON2017_HAB_AMINUTUM (PRJEB18614) + * + * Claimed with `aree start-study`. Fill in params for the workflow this + * study runs (see config/IOCAS2022_OA_ENERGY.config for RNA-seq and + * config/CIBNOR2021_HEAT_RRSS.config for methylation), then + * + * nextflow run workflows/ -config config/PAYTON2017_HAB_AMINUTUM.config -profile local,workstation + * + * Generate the sample sheet and FASTQ manifest rather than writing them: + * + * aree fetch-samplesheet --bioproject PRJEB18614 --study PAYTON2017_HAB_AMINUTUM --condition-attribute + */ + +includeConfig 'base.config' + +params { + mode = 'raw_reanalysis' + + sample_sheet = 'data/studies/PAYTON2017_HAB_AMINUTUM/samplesheet.tsv' + reads = 'data/raw/PAYTON2017_HAB_AMINUTUM/*_{1,2}.fastq.gz' + outdir = 'results/PAYTON2017_HAB_AMINUTUM' +} diff --git a/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml b/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml new file mode 100644 index 0000000..6cd3800 --- /dev/null +++ b/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml @@ -0,0 +1,62 @@ +# Copy this file to registry/studies/.yaml and fill in every field. +# Validate with: aree validate-study registry/studies/.yaml +# See docs/adding_a_study.md for field-by-field guidance. + +study_id: PAYTON2017_HAB_AMINUTUM +simulated: false + +accessions: + doi: null + bioproject: "PRJEB18614" + geo: null + sra: null + ena: null + proteomexchange: null + other: null + +citation: "Author A, Author B (YEAR). Title. Journal. https://doi.org/..." +species: "Crassostrea gigas" +strain_or_population: null +genome_assembly: "cgigas_uk_roslin_v1" +annotation_version: null + +assay_type: ["rnaseq"] +analysis_mode: "processed_results_harmonization" # or raw_reanalysis +platform: null + +data_availability: + raw_data_available: false + processed_data_available: true + status: "available" # available | restricted | embargoed | unavailable + access_notes: null + +qc_status: "not_started" +analysis_status: "not_started" + +comparisons: + - comparison_id: "comp1" + tissue: "gill" + life_stage: "adult" + stressor_original: "exact wording from the source paper" + stressor_standardized: "temperature" + exposure_intensity: null + exposure_duration: null + exposure_timing: null + control_condition: "describe control arm" + treatment_condition: "describe treatment arm" + phenotype: "thermal_tolerance" + phenotype_direction: "decrease" + phenotype_unit: null + resilience_classification: "resilience" + sample_size: 0 + biological_replicates: 0 + results_file: null + +quality_flags: [] +limitations: null + +provenance: + registered_by: "sr320" + date_registered: "2026-10-11" + curation_notes: null + source_links: [] From 5f010a45570c28e58ee89d485afc28d5327b8aaf Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Sun, 11 Oct 2026 18:55:20 -0700 Subject: [PATCH 2/4] Register PAYTON2017_HAB_AMINUTUM (PRJEB18614): design, comparison Payton et al. 2017 Alexandrium minutum HAB exposure, adult gill, 13 pooled libraries per diet on two lanes each. Diet from ENA growth condition, cross-checked against the committed ArrayExpress SDRF; lanes summed with replicate_unit = sample_accession. Uses toxicant_tolerance (PR #31). Run not yet done. Co-Authored-By: Claude Opus 5.5 --- config/PAYTON2017_HAB_AMINUTUM.config | 59 ++++++-- .../E-MTAB-5345.sdrf.txt | 105 ++++++++++++++ .../ena_provenance.json | 89 ++++++++++++ .../fastq_manifest.tsv | 105 ++++++++++++++ .../PAYTON2017_HAB_AMINUTUM/samplesheet.tsv | 53 +++++++ registry/studies/PAYTON2017_HAB_AMINUTUM.yaml | 136 +++++++++++++----- tests/test_payton2017_hab_study.py | 95 ++++++++++++ 7 files changed, 597 insertions(+), 45 deletions(-) create mode 100644 data/studies/PAYTON2017_HAB_AMINUTUM/E-MTAB-5345.sdrf.txt create mode 100644 data/studies/PAYTON2017_HAB_AMINUTUM/ena_provenance.json create mode 100644 data/studies/PAYTON2017_HAB_AMINUTUM/fastq_manifest.tsv create mode 100644 data/studies/PAYTON2017_HAB_AMINUTUM/samplesheet.tsv create mode 100644 tests/test_payton2017_hab_study.py diff --git a/config/PAYTON2017_HAB_AMINUTUM.config b/config/PAYTON2017_HAB_AMINUTUM.config index deefa91..08d35cd 100644 --- a/config/PAYTON2017_HAB_AMINUTUM.config +++ b/config/PAYTON2017_HAB_AMINUTUM.config @@ -1,15 +1,23 @@ /* * AREE :: run configuration for PAYTON2017_HAB_AMINUTUM (PRJEB18614) * - * Claimed with `aree start-study`. Fill in params for the workflow this - * study runs (see config/IOCAS2022_OA_ENERGY.config for RNA-seq and - * config/CIBNOR2021_HEAT_RRSS.config for methylation), then + * Payton et al. 2017, Sci Rep 7:3480 (doi:10.1038/s41598-017-03797-4); + * ArrayExpress E-MTAB-5345. Adult gill, 6 days on the paralytic-shellfish- + * toxin producer Alexandrium minutum (HAB, ~400 cells/mL) vs the non-toxic + * dinoflagellate Heterocapsa triquetra, 3 tanks per diet; gill of 6 oysters + * pooled per diet every 4 h for 52 h (13 libraries per diet), each library + * sequenced on two lanes (52 runs). * - * nextflow run workflows/ -config config/PAYTON2017_HAB_AMINUTUM.config -profile local,workstation + * nextflow run workflows/rnaseq -config config/PAYTON2017_HAB_AMINUTUM.config \ + * -profile local,workstation * - * Generate the sample sheet and FASTQ manifest rather than writing them: + * Every run gets its own sample_id (the run accession), and + * replicate_unit = sample_accession sums each library's two lanes before + * DESeq2, so the replicates are the 13 libraries per diet, not 26 lanes. * - * aree fetch-samplesheet --bioproject PRJEB18614 --study PAYTON2017_HAB_AMINUTUM --condition-attribute + * aree fetch-samplesheet --bioproject PRJEB18614 --study PAYTON2017_HAB_AMINUTUM \ + * --label-field run_accession --label-pattern '^(?PERR\d+)$' \ + * --condition-attribute "growth condition" --attribute "organism part" */ includeConfig 'base.config' @@ -17,7 +25,42 @@ includeConfig 'base.config' params { mode = 'raw_reanalysis' + rnaseq { + study_id = 'PAYTON2017_HAB_AMINUTUM' + // Null so --comparison_id on the command line takes effect. + comparison_id = null + genome_assembly = 'GCF_963853765.1' + annotation_version = 'GCF_963853765.1-RS_2024_06' + processed_results = null + } + + comparison_id = 'alexandrium_vs_heterocapsa_6d' + sample_sheet = 'data/studies/PAYTON2017_HAB_AMINUTUM/samplesheet.tsv' - reads = 'data/raw/PAYTON2017_HAB_AMINUTUM/*_{1,2}.fastq.gz' - outdir = 'results/PAYTON2017_HAB_AMINUTUM' + + control_level = 'Heterocapsa_triquetra' + treatment_level = 'Alexandrium_minutum' + + // Two sequencing lanes per library: sum them, so a library is one replicate. + replicate_unit = 'sample_accession' + + // FASTQ are not committed. Verify against ENA's MD5s: + // awk -F'\t' 'NR>1 {print $4" "$1"_"$2".fastq.gz"}' \ + // data/studies/PAYTON2017_HAB_AMINUTUM/fastq_manifest.tsv > md5sums.txt && md5sum -c md5sums.txt + reads = 'data/raw/PAYTON2017_HAB_AMINUTUM/ERR*_{1,2}.fastq.gz' + + transcript_fasta = 'data/reference/GCF_963853765.1/rna.fna' + gtf = 'data/reference/GCF_963853765.1/genomic.gtf' + tx2gene = 'data/reference/GCF_963853765.1/tx2gene.tsv' + salmon_index = null + + outdir = 'results/rnaseq/PAYTON2017_HAB_AMINUTUM' +} + +process { + // 52 HiSeq 2500 2x100 runs (26 libraries x 2 lanes). Sized for a 16 GB machine. + withName: 'SALMON_INDEX' { cpus = 8; memory = '12 GB'; time = '4h' } + withName: 'SALMON_QUANT' { cpus = 8; memory = '12 GB'; time = '2h' } + withName: 'TRIM_FASTP' { cpus = 4; memory = '8 GB'; time = '2h' } + withName: 'FASTQC' { cpus = 2; memory = '4 GB'; time = '1h' } } diff --git a/data/studies/PAYTON2017_HAB_AMINUTUM/E-MTAB-5345.sdrf.txt b/data/studies/PAYTON2017_HAB_AMINUTUM/E-MTAB-5345.sdrf.txt new file mode 100644 index 0000000..e57dc4f --- /dev/null +++ b/data/studies/PAYTON2017_HAB_AMINUTUM/E-MTAB-5345.sdrf.txt @@ -0,0 +1,105 @@ +Source Name Comment[ENA_SAMPLE] Comment[BioSD_SAMPLE] Characteristics[organism] Characteristics[feeding condition] Characteristics[organism part] Material Type Protocol REF Protocol REF Protocol REF Extract Name Material Type Comment[LIBRARY_LAYOUT] Comment[LIBRARY_SELECTION] Comment[LIBRARY_SOURCE] Comment[LIBRARY_STRAND] Comment[LIBRARY_STRATEGY] Comment[NOMINAL_LENGTH] Comment[NOMINAL_SDEV] Comment[ORIENTATION] Protocol REF Performer Assay Name Technology Type Comment[ENA_EXPERIMENT] Scan Name Comment[SUBMITTED_FILE_NAME] Comment[ENA_RUN] Comment[FASTQ_URI] Comment[SPOT_LENGTH] Comment[READ_INDEX_1_BASE_COORD] Factor Value[feeding condition] Factor Value[time] Unit[time unit] +Sample 16 ERS1473698 SAMEA26687668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 16 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3A_ACAGTG_L003 sequencing assay ERX1825482 3A_ACAGTG_L003_1.fq.gz 3A_ACAGTG_L003_1.fq.gz ERR1758942 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758942/ERR1758942_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 12.5 hour +Sample 16 ERS1473698 SAMEA26687668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 16 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3A_ACAGTG_L003 sequencing assay ERX1825482 3A_ACAGTG_L003_2.fq.gz 3A_ACAGTG_L003_2.fq.gz ERR1758942 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758942/ERR1758942_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 12.5 hour +Sample 16 ERS1473698 SAMEA26687668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 16 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3A_ACAGTG_L004 sequencing assay ERX1825482 3A_ACAGTG_L004_1.fq.gz 3A_ACAGTG_L004_1.fq.gz ERR1758943 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758943/ERR1758943_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 12.5 hour +Sample 16 ERS1473698 SAMEA26687668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 16 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3A_ACAGTG_L004 sequencing assay ERX1825482 3A_ACAGTG_L004_2.fq.gz 3A_ACAGTG_L004_2.fq.gz ERR1758943 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758943/ERR1758943_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 12.5 hour +Sample 3 ERS1473699 SAMEA26688418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 3 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3H_TGACCA_L001 sequencing assay ERX1825483 3H_TGACCA_L001_2.fq.gz 3H_TGACCA_L001_2.fq.gz ERR1758944 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758944/ERR1758944_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 12.5 hour +Sample 3 ERS1473699 SAMEA26688418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 3 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3H_TGACCA_L001 sequencing assay ERX1825483 3H_TGACCA_L001_1.fq.gz 3H_TGACCA_L001_1.fq.gz ERR1758944 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758944/ERR1758944_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 12.5 hour +Sample 3 ERS1473699 SAMEA26688418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 3 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3H_TGACCA_L002 sequencing assay ERX1825483 3H_TGACCA_L002_1.fq.gz 3H_TGACCA_L002_1.fq.gz ERR1758945 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758945/ERR1758945_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 12.5 hour +Sample 3 ERS1473699 SAMEA26688418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 3 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 3H_TGACCA_L002 sequencing assay ERX1825483 3H_TGACCA_L002_2.fq.gz 3H_TGACCA_L002_2.fq.gz ERR1758945 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758945/ERR1758945_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 12.5 hour +Sample 17 ERS1473700 SAMEA26689168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 17 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4A_CAGATC_L005 sequencing assay ERX1825484 4A_CAGATC_L005_1.fq.gz 4A_CAGATC_L005_1.fq.gz ERR1758946 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758946/ERR1758946_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 16.5 hour +Sample 17 ERS1473700 SAMEA26689168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 17 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4A_CAGATC_L005 sequencing assay ERX1825484 4A_CAGATC_L005_2.fq.gz 4A_CAGATC_L005_2.fq.gz ERR1758946 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758946/ERR1758946_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 16.5 hour +Sample 17 ERS1473700 SAMEA26689168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 17 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4A_CAGATC_L006 sequencing assay ERX1825484 4A_CAGATC_L006_1.fq.gz 4A_CAGATC_L006_1.fq.gz ERR1758947 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758947/ERR1758947_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 16.5 hour +Sample 17 ERS1473700 SAMEA26689168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 17 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4A_CAGATC_L006 sequencing assay ERX1825484 4A_CAGATC_L006_2.fq.gz 4A_CAGATC_L006_2.fq.gz ERR1758947 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758947/ERR1758947_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 16.5 hour +Sample 4 ERS1473701 SAMEA26689918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 4 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4H_ACAGTG_L001 sequencing assay ERX1825485 4H_ACAGTG_L001_1.fq.gz 4H_ACAGTG_L001_1.fq.gz ERR1758948 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758948/ERR1758948_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 16.5 hour +Sample 4 ERS1473701 SAMEA26689918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 4 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4H_ACAGTG_L001 sequencing assay ERX1825485 4H_ACAGTG_L001_2.fq.gz 4H_ACAGTG_L001_2.fq.gz ERR1758948 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758948/ERR1758948_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 16.5 hour +Sample 4 ERS1473701 SAMEA26689918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 4 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4H_ACAGTG_L002 sequencing assay ERX1825485 4H_ACAGTG_L002_1.fq.gz 4H_ACAGTG_L002_1.fq.gz ERR1758949 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758949/ERR1758949_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 16.5 hour +Sample 4 ERS1473701 SAMEA26689918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 4 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 4H_ACAGTG_L002 sequencing assay ERX1825485 4H_ACAGTG_L002_2.fq.gz 4H_ACAGTG_L002_2.fq.gz ERR1758949 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758949/ERR1758949_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 16.5 hour +Sample 18 ERS1473702 SAMEA26690668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 18 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5A_GCCAAT_L001 sequencing assay ERX1825486 5A_GCCAAT_L001_1.fq.gz 5A_GCCAAT_L001_1.fq.gz ERR1758950 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758950/ERR1758950_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 20.5 hour +Sample 18 ERS1473702 SAMEA26690668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 18 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5A_GCCAAT_L001 sequencing assay ERX1825486 5A_GCCAAT_L001_2.fq.gz 5A_GCCAAT_L001_2.fq.gz ERR1758950 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758950/ERR1758950_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 20.5 hour +Sample 18 ERS1473702 SAMEA26690668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 18 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5A_GCCAAT_L002 sequencing assay ERX1825486 5A_GCCAAT_L002_1.fq.gz 5A_GCCAAT_L002_1.fq.gz ERR1758951 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758951/ERR1758951_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 20.5 hour +Sample 18 ERS1473702 SAMEA26690668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 18 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5A_GCCAAT_L002 sequencing assay ERX1825486 5A_GCCAAT_L002_2.fq.gz 5A_GCCAAT_L002_2.fq.gz ERR1758951 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758951/ERR1758951_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 20.5 hour +Sample 5 ERS1473703 SAMEA26691418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 5 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5H_CTTGTA_L005 sequencing assay ERX1825487 5H_CTTGTA_L005_1.fq.gz 5H_CTTGTA_L005_1.fq.gz ERR1758952 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758952/ERR1758952_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 20.5 hour +Sample 5 ERS1473703 SAMEA26691418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 5 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5H_CTTGTA_L005 sequencing assay ERX1825487 5H_CTTGTA_L005_2.fq.gz 5H_CTTGTA_L005_2.fq.gz ERR1758952 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758952/ERR1758952_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 20.5 hour +Sample 5 ERS1473703 SAMEA26691418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 5 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5H_CTTGTA_L006 sequencing assay ERX1825487 5H_CTTGTA_L006_1.fq.gz 5H_CTTGTA_L006_1.fq.gz ERR1758953 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758953/ERR1758953_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 20.5 hour +Sample 5 ERS1473703 SAMEA26691418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 5 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 5H_CTTGTA_L006 sequencing assay ERX1825487 5H_CTTGTA_L006_2.fq.gz 5H_CTTGTA_L006_2.fq.gz ERR1758953 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758953/ERR1758953_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 20.5 hour +Sample 1 ERS1473704 SAMEA26692168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 1 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1H_ATCACG_L001 sequencing assay ERX1825488 1H_ATCACG_L001_1.fq.gz 1H_ATCACG_L001_1.fq.gz ERR1758954 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758954/ERR1758954_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 4.5 hour +Sample 1 ERS1473704 SAMEA26692168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 1 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1H_ATCACG_L001 sequencing assay ERX1825488 1H_ATCACG_L001_2.fq.gz 1H_ATCACG_L001_2.fq.gz ERR1758954 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758954/ERR1758954_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 4.5 hour +Sample 1 ERS1473704 SAMEA26692168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 1 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1H_ATCACG_L002 sequencing assay ERX1825488 1H_ATCACG_L002_1.fq.gz 1H_ATCACG_L002_1.fq.gz ERR1758955 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758955/ERR1758955_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 4.5 hour +Sample 1 ERS1473704 SAMEA26692168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 1 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1H_ATCACG_L002 sequencing assay ERX1825488 1H_ATCACG_L002_2.fq.gz 1H_ATCACG_L002_2.fq.gz ERR1758955 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758955/ERR1758955_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 4.5 hour +Sample 14 ERS1473705 SAMEA26692918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 14 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1A_ATCACG_L003 sequencing assay ERX1825489 1A_ATCACG_L003_1.fq.gz 1A_ATCACG_L003_1.fq.gz ERR1758956 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758956/ERR1758956_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 4.5 hour +Sample 14 ERS1473705 SAMEA26692918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 14 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1A_ATCACG_L003 sequencing assay ERX1825489 1A_ATCACG_L003_2.fq.gz 1A_ATCACG_L003_2.fq.gz ERR1758956 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758956/ERR1758956_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 4.5 hour +Sample 14 ERS1473705 SAMEA26692918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 14 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1A_ATCACG_L004 sequencing assay ERX1825489 1A_ATCACG_L004_1.fq.gz 1A_ATCACG_L004_1.fq.gz ERR1758957 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758957/ERR1758957_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 4.5 hour +Sample 14 ERS1473705 SAMEA26692918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 14 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 1A_ATCACG_L004 sequencing assay ERX1825489 1A_ATCACG_L004_2.fq.gz 1A_ATCACG_L004_2.fq.gz ERR1758957 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758957/ERR1758957_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 4.5 hour +Sample 15 ERS1473706 SAMEA26693668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 15 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2A_TGACCA_L003 sequencing assay ERX1825490 2A_TGACCA_L003_1.fq.gz 2A_TGACCA_L003_1.fq.gz ERR1758958 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758958/ERR1758958_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 8.5 hour +Sample 15 ERS1473706 SAMEA26693668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 15 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2A_TGACCA_L003 sequencing assay ERX1825490 2A_TGACCA_L003_2.fq.gz 2A_TGACCA_L003_2.fq.gz ERR1758958 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758958/ERR1758958_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 8.5 hour +Sample 15 ERS1473706 SAMEA26693668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 15 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2A_TGACCA_L004 sequencing assay ERX1825490 2A_TGACCA_L004_1.fq.gz 2A_TGACCA_L004_1.fq.gz ERR1758959 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758959/ERR1758959_1.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 8.5 hour +Sample 15 ERS1473706 SAMEA26693668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 15 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2A_TGACCA_L004 sequencing assay ERX1825490 2A_TGACCA_L004_2.fq.gz 2A_TGACCA_L004_2.fq.gz ERR1758959 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758959/ERR1758959_2.fastq.gz 200 101 Alexandrium minutum Day 1 ZT 8.5 hour +Sample 2 ERS1473707 SAMEA26694418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 2 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2H_TTAGGC_L001 sequencing assay ERX1825491 2H_TTAGGC_L001_1.fq.gz 2H_TTAGGC_L001_1.fq.gz ERR1758960 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758960/ERR1758960_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 8.5 hour +Sample 2 ERS1473707 SAMEA26694418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 2 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2H_TTAGGC_L001 sequencing assay ERX1825491 2H_TTAGGC_L001_2.fq.gz 2H_TTAGGC_L001_2.fq.gz ERR1758960 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758960/ERR1758960_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 8.5 hour +Sample 2 ERS1473707 SAMEA26694418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 2 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2H_TTAGGC_L002 sequencing assay ERX1825491 2H_TTAGGC_L002_1.fq.gz 2H_TTAGGC_L002_1.fq.gz ERR1758961 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758961/ERR1758961_1.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 8.5 hour +Sample 2 ERS1473707 SAMEA26694418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 2 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 2H_TTAGGC_L002 sequencing assay ERX1825491 2H_TTAGGC_L002_2.fq.gz 2H_TTAGGC_L002_2.fq.gz ERR1758961 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758961/ERR1758961_2.fastq.gz 200 101 Heterocapsa triquetra Day 1 ZT 8.5 hour +Sample 19 ERS1473708 SAMEA26695168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 19 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6A_CAGATC_L001 sequencing assay ERX1825492 6A_CAGATC_L001_1.fq.gz 6A_CAGATC_L001_1.fq.gz ERR1758962 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758962/ERR1758962_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 0.5 hour +Sample 19 ERS1473708 SAMEA26695168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 19 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6A_CAGATC_L001 sequencing assay ERX1825492 6A_CAGATC_L001_2.fq.gz 6A_CAGATC_L001_2.fq.gz ERR1758962 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758962/ERR1758962_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 0.5 hour +Sample 19 ERS1473708 SAMEA26695168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 19 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6A_CAGATC_L002 sequencing assay ERX1825492 6A_CAGATC_L002_1.fq.gz 6A_CAGATC_L002_1.fq.gz ERR1758963 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758963/ERR1758963_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 0.5 hour +Sample 19 ERS1473708 SAMEA26695168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 19 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6A_CAGATC_L002 sequencing assay ERX1825492 6A_CAGATC_L002_2.fq.gz 6A_CAGATC_L002_2.fq.gz ERR1758963 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758963/ERR1758963_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 0.5 hour +Sample 6 ERS1473709 SAMEA26695918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 6 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6H_GTCCGC_L005 sequencing assay ERX1825493 6H_GTCCGC_L005_1.fq.gz 6H_GTCCGC_L005_1.fq.gz ERR1758964 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758964/ERR1758964_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 0.5 hour +Sample 6 ERS1473709 SAMEA26695918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 6 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6H_GTCCGC_L005 sequencing assay ERX1825493 6H_GTCCGC_L005_2.fq.gz 6H_GTCCGC_L005_2.fq.gz ERR1758964 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758964/ERR1758964_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 0.5 hour +Sample 6 ERS1473709 SAMEA26695918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 6 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6H_GTCCGC_L006 sequencing assay ERX1825493 6H_GTCCGC_L006_1.fq.gz 6H_GTCCGC_L006_1.fq.gz ERR1758965 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758965/ERR1758965_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 0.5 hour +Sample 6 ERS1473709 SAMEA26695918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 6 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 6H_GTCCGC_L006 sequencing assay ERX1825493 6H_GTCCGC_L006_2.fq.gz 6H_GTCCGC_L006_2.fq.gz ERR1758965 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758965/ERR1758965_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 0.5 hour +Sample 22 ERS1473710 SAMEA26696668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 22 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9A_GTTTCG_L003 sequencing assay ERX1825494 9A_GTTTCG_L003_1.fq.gz 9A_GTTTCG_L003_1.fq.gz ERR1758966 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758966/ERR1758966_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 12.5 hour +Sample 22 ERS1473710 SAMEA26696668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 22 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9A_GTTTCG_L003 sequencing assay ERX1825494 9A_GTTTCG_L003_2.fq.gz 9A_GTTTCG_L003_2.fq.gz ERR1758966 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758966/ERR1758966_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 12.5 hour +Sample 22 ERS1473710 SAMEA26696668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 22 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9A_GTTTCG_L004 sequencing assay ERX1825494 9A_GTTTCG_L004_1.fq.gz 9A_GTTTCG_L004_1.fq.gz ERR1758967 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758967/ERR1758967_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 12.5 hour +Sample 22 ERS1473710 SAMEA26696668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 22 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9A_GTTTCG_L004 sequencing assay ERX1825494 9A_GTTTCG_L004_2.fq.gz 9A_GTTTCG_L004_2.fq.gz ERR1758967 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758967/ERR1758967_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 12.5 hour +Sample 9 ERS1473711 SAMEA26697418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 9 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9H_ACTGAT_L005 sequencing assay ERX1825495 9H_ACTGAT_L005_1.fq.gz 9H_ACTGAT_L005_1.fq.gz ERR1758968 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758968/ERR1758968_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 12.5 hour +Sample 9 ERS1473711 SAMEA26697418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 9 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9H_ACTGAT_L005 sequencing assay ERX1825495 9H_ACTGAT_L005_2.fq.gz 9H_ACTGAT_L005_2.fq.gz ERR1758968 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758968/ERR1758968_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 12.5 hour +Sample 9 ERS1473711 SAMEA26697418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 9 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9H_ACTGAT_L006 sequencing assay ERX1825495 9H_ACTGAT_L006_1.fq.gz 9H_ACTGAT_L006_1.fq.gz ERR1758969 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758969/ERR1758969_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 12.5 hour +Sample 9 ERS1473711 SAMEA26697418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 9 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 9H_ACTGAT_L006 sequencing assay ERX1825495 9H_ACTGAT_L006_2.fq.gz 9H_ACTGAT_L006_2.fq.gz ERR1758969 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758969/ERR1758969_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 12.5 hour +Sample 10 ERS1473712 SAMEA26698168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 10 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10H_CGATGT_L005 sequencing assay ERX1825496 10H_CGATGT_L005_1.fq.gz 10H_CGATGT_L005_1.fq.gz ERR1758970 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758970/ERR1758970_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 16.5 hour +Sample 10 ERS1473712 SAMEA26698168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 10 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10H_CGATGT_L005 sequencing assay ERX1825496 10H_CGATGT_L005_2.fq.gz 10H_CGATGT_L005_2.fq.gz ERR1758970 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758970/ERR1758970_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 16.5 hour +Sample 10 ERS1473712 SAMEA26698168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 10 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10H_CGATGT_L006 sequencing assay ERX1825496 10H_CGATGT_L006_1.fq.gz 10H_CGATGT_L006_1.fq.gz ERR1758971 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758971/ERR1758971_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 16.5 hour +Sample 10 ERS1473712 SAMEA26698168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 10 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10H_CGATGT_L006 sequencing assay ERX1825496 10H_CGATGT_L006_2.fq.gz 10H_CGATGT_L006_2.fq.gz ERR1758971 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758971/ERR1758971_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 16.5 hour +Sample 23 ERS1473713 SAMEA26698918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 23 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10A_TTAGGC_L007 sequencing assay ERX1825497 10A_TTAGGC_L007_1.fq.gz 10A_TTAGGC_L007_1.fq.gz ERR1758972 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758972/ERR1758972_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 16.5 hour +Sample 23 ERS1473713 SAMEA26698918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 23 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10A_TTAGGC_L007 sequencing assay ERX1825497 10A_TTAGGC_L007_2.fq.gz 10A_TTAGGC_L007_2.fq.gz ERR1758972 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758972/ERR1758972_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 16.5 hour +Sample 23 ERS1473713 SAMEA26698918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 23 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10A_TTAGGC_L008 sequencing assay ERX1825497 10A_TTAGGC_L008_1.fq.gz 10A_TTAGGC_L008_1.fq.gz ERR1758973 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758973/ERR1758973_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 16.5 hour +Sample 23 ERS1473713 SAMEA26698918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 23 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 10A_TTAGGC_L008 sequencing assay ERX1825497 10A_TTAGGC_L008_2.fq.gz 10A_TTAGGC_L008_2.fq.gz ERR1758973 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758973/ERR1758973_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 16.5 hour +Sample 11 ERS1473714 SAMEA26699668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 11 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11H_TGACCA_L007 sequencing assay ERX1825498 11H_TGACCA_L007_1.fq.gz 11H_TGACCA_L007_1.fq.gz ERR1758974 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758974/ERR1758974_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 20.5 hour +Sample 11 ERS1473714 SAMEA26699668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 11 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11H_TGACCA_L007 sequencing assay ERX1825498 11H_TGACCA_L007_2.fq.gz 11H_TGACCA_L007_2.fq.gz ERR1758974 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758974/ERR1758974_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 20.5 hour +Sample 11 ERS1473714 SAMEA26699668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 11 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11H_TGACCA_L008 sequencing assay ERX1825498 11H_TGACCA_L008_1.fq.gz 11H_TGACCA_L008_1.fq.gz ERR1758975 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758975/ERR1758975_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 20.5 hour +Sample 11 ERS1473714 SAMEA26699668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 11 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11H_TGACCA_L008 sequencing assay ERX1825498 11H_TGACCA_L008_2.fq.gz 11H_TGACCA_L008_2.fq.gz ERR1758975 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758975/ERR1758975_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 20.5 hour +Sample 24 ERS1473715 SAMEA26700418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 24 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11A_GCCAAT_L007 sequencing assay ERX1825499 11A_GCCAAT_L007_1.fq.gz 11A_GCCAAT_L007_1.fq.gz ERR1758976 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758976/ERR1758976_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 20.5 hour +Sample 24 ERS1473715 SAMEA26700418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 24 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11A_GCCAAT_L007 sequencing assay ERX1825499 11A_GCCAAT_L007_2.fq.gz 11A_GCCAAT_L007_2.fq.gz ERR1758976 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758976/ERR1758976_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 20.5 hour +Sample 24 ERS1473715 SAMEA26700418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 24 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11A_GCCAAT_L008 sequencing assay ERX1825499 11A_GCCAAT_L008_1.fq.gz 11A_GCCAAT_L008_1.fq.gz ERR1758977 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758977/ERR1758977_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 20.5 hour +Sample 24 ERS1473715 SAMEA26700418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 24 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 11A_GCCAAT_L008 sequencing assay ERX1825499 11A_GCCAAT_L008_2.fq.gz 11A_GCCAAT_L008_2.fq.gz ERR1758977 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758977/ERR1758977_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 20.5 hour +Sample 20 ERS1473716 SAMEA26701168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 20 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7A_TAGCTT_L003 sequencing assay ERX1825500 7A_TAGCTT_L003_1.fq.gz 7A_TAGCTT_L003_1.fq.gz ERR1758978 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758978/ERR1758978_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 4.5 hour +Sample 20 ERS1473716 SAMEA26701168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 20 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7A_TAGCTT_L003 sequencing assay ERX1825500 7A_TAGCTT_L003_2.fq.gz 7A_TAGCTT_L003_2.fq.gz ERR1758978 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758978/ERR1758978_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 4.5 hour +Sample 20 ERS1473716 SAMEA26701168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 20 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7A_TAGCTT_L004 sequencing assay ERX1825500 7A_TAGCTT_L004_1.fq.gz 7A_TAGCTT_L004_1.fq.gz ERR1758979 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758979/ERR1758979_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 4.5 hour +Sample 20 ERS1473716 SAMEA26701168 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 20 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7A_TAGCTT_L004 sequencing assay ERX1825500 7A_TAGCTT_L004_2.fq.gz 7A_TAGCTT_L004_2.fq.gz ERR1758979 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758979/ERR1758979_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 4.5 hour +Sample 7 ERS1473717 SAMEA26701918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 7 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7H_GTGGCC_L006 sequencing assay ERX1825501 7H_GTGGCC_L006_2.fq.gz 7H_GTGGCC_L006_2.fq.gz ERR1758980 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758980/ERR1758980_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 4.5 hour +Sample 7 ERS1473717 SAMEA26701918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 7 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7H_GTGGCC_L005 sequencing assay ERX1825501 7H_GTGGCC_L005_1.fq.gz 7H_GTGGCC_L005_1.fq.gz ERR1758981 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758981/ERR1758981_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 4.5 hour +Sample 7 ERS1473717 SAMEA26701918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 7 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7H_GTGGCC_L005 sequencing assay ERX1825501 7H_GTGGCC_L005_2.fq.gz 7H_GTGGCC_L005_2.fq.gz ERR1758981 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758981/ERR1758981_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 4.5 hour +Sample 7 ERS1473717 SAMEA26701918 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 7 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 7H_GTGGCC_L006 sequencing assay ERX1825501 7H_GTGGCC_L006_1.fq.gz 7H_GTGGCC_L006_1.fq.gz ERR1758980 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758980/ERR1758980_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 4.5 hour +Sample 21 ERS1473718 SAMEA26702668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 21 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8A_ATGTCA_L003 sequencing assay ERX1825502 8A_ATGTCA_L003_1.fq.gz 8A_ATGTCA_L003_1.fq.gz ERR1758982 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758982/ERR1758982_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 8.5 hour +Sample 21 ERS1473718 SAMEA26702668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 21 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8A_ATGTCA_L003 sequencing assay ERX1825502 8A_ATGTCA_L003_2.fq.gz 8A_ATGTCA_L003_2.fq.gz ERR1758982 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758982/ERR1758982_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 8.5 hour +Sample 21 ERS1473718 SAMEA26702668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 21 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8A_ATGTCA_L004 sequencing assay ERX1825502 8A_ATGTCA_L004_1.fq.gz 8A_ATGTCA_L004_1.fq.gz ERR1758983 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758983/ERR1758983_1.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 8.5 hour +Sample 21 ERS1473718 SAMEA26702668 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 21 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8A_ATGTCA_L004 sequencing assay ERX1825502 8A_ATGTCA_L004_2.fq.gz 8A_ATGTCA_L004_2.fq.gz ERR1758983 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758983/ERR1758983_2.fastq.gz 200 101 Alexandrium minutum Day 2 ZT 8.5 hour +Sample 8 ERS1473719 SAMEA26703418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 8 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8H_GAGTGG_L005 sequencing assay ERX1825503 8H_GAGTGG_L005_1.fq.gz 8H_GAGTGG_L005_1.fq.gz ERR1758984 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758984/ERR1758984_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 8.5 hour +Sample 8 ERS1473719 SAMEA26703418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 8 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8H_GAGTGG_L005 sequencing assay ERX1825503 8H_GAGTGG_L005_2.fq.gz 8H_GAGTGG_L005_2.fq.gz ERR1758984 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/004/ERR1758984/ERR1758984_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 8.5 hour +Sample 8 ERS1473719 SAMEA26703418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 8 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8H_GAGTGG_L006 sequencing assay ERX1825503 8H_GAGTGG_L006_1.fq.gz 8H_GAGTGG_L006_1.fq.gz ERR1758985 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758985/ERR1758985_1.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 8.5 hour +Sample 8 ERS1473719 SAMEA26703418 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 8 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 8H_GAGTGG_L006 sequencing assay ERX1825503 8H_GAGTGG_L006_2.fq.gz 8H_GAGTGG_L006_2.fq.gz ERR1758985 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/005/ERR1758985/ERR1758985_2.fastq.gz 200 101 Heterocapsa triquetra Day 2 ZT 8.5 hour +Sample 12 ERS1473720 SAMEA26704168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 12 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12H_CAGATC_L007 sequencing assay ERX1825504 12H_CAGATC_L007_1.fq.gz 12H_CAGATC_L007_1.fq.gz ERR1758986 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758986/ERR1758986_1.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 0.5 hour +Sample 12 ERS1473720 SAMEA26704168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 12 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12H_CAGATC_L007 sequencing assay ERX1825504 12H_CAGATC_L007_2.fq.gz 12H_CAGATC_L007_2.fq.gz ERR1758986 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/006/ERR1758986/ERR1758986_2.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 0.5 hour +Sample 12 ERS1473720 SAMEA26704168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 12 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12H_CAGATC_L008 sequencing assay ERX1825504 12H_CAGATC_L008_1.fq.gz 12H_CAGATC_L008_1.fq.gz ERR1758987 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758987/ERR1758987_1.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 0.5 hour +Sample 12 ERS1473720 SAMEA26704168 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 12 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12H_CAGATC_L008 sequencing assay ERX1825504 12H_CAGATC_L008_2.fq.gz 12H_CAGATC_L008_2.fq.gz ERR1758987 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/007/ERR1758987/ERR1758987_2.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 0.5 hour +Sample 25 ERS1473721 SAMEA26704918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 25 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12A_GATCAG_L007 sequencing assay ERX1825505 12A_GATCAG_L007_1.fq.gz 12A_GATCAG_L007_1.fq.gz ERR1758988 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758988/ERR1758988_1.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 0.5 hour +Sample 25 ERS1473721 SAMEA26704918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 25 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12A_GATCAG_L007 sequencing assay ERX1825505 12A_GATCAG_L007_2.fq.gz 12A_GATCAG_L007_2.fq.gz ERR1758988 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/008/ERR1758988/ERR1758988_2.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 0.5 hour +Sample 25 ERS1473721 SAMEA26704918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 25 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12A_GATCAG_L008 sequencing assay ERX1825505 12A_GATCAG_L008_1.fq.gz 12A_GATCAG_L008_1.fq.gz ERR1758989 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758989/ERR1758989_1.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 0.5 hour +Sample 25 ERS1473721 SAMEA26704918 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 25 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 12A_GATCAG_L008 sequencing assay ERX1825505 12A_GATCAG_L008_2.fq.gz 12A_GATCAG_L008_2.fq.gz ERR1758989 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/009/ERR1758989/ERR1758989_2.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 0.5 hour +Sample 13 ERS1473722 SAMEA26705668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 13 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13H_CTTGTA_L007 sequencing assay ERX1825506 13H_CTTGTA_L007_1.fq.gz 13H_CTTGTA_L007_1.fq.gz ERR1758990 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758990/ERR1758990_1.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 4.5 hour +Sample 13 ERS1473722 SAMEA26705668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 13 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13H_CTTGTA_L007 sequencing assay ERX1825506 13H_CTTGTA_L007_2.fq.gz 13H_CTTGTA_L007_2.fq.gz ERR1758990 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/000/ERR1758990/ERR1758990_2.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 4.5 hour +Sample 13 ERS1473722 SAMEA26705668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 13 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13H_CTTGTA_L008 sequencing assay ERX1825506 13H_CTTGTA_L008_1.fq.gz 13H_CTTGTA_L008_1.fq.gz ERR1758991 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758991/ERR1758991_1.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 4.5 hour +Sample 13 ERS1473722 SAMEA26705668 Crassostrea gigas Heterocapsa triquetra gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 13 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13H_CTTGTA_L008 sequencing assay ERX1825506 13H_CTTGTA_L008_2.fq.gz 13H_CTTGTA_L008_2.fq.gz ERR1758991 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/001/ERR1758991/ERR1758991_2.fastq.gz 200 101 Heterocapsa triquetra Day 3 ZT 4.5 hour +Sample 26 ERS1473723 SAMEA26706418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 26 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13A_ACTGAT_L007 sequencing assay ERX1825507 13A_ACTGAT_L007_1.fq.gz 13A_ACTGAT_L007_1.fq.gz ERR1758992 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758992/ERR1758992_1.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 4.5 hour +Sample 26 ERS1473723 SAMEA26706418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 26 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13A_ACTGAT_L007 sequencing assay ERX1825507 13A_ACTGAT_L007_2.fq.gz 13A_ACTGAT_L007_2.fq.gz ERR1758992 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/002/ERR1758992/ERR1758992_2.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 4.5 hour +Sample 26 ERS1473723 SAMEA26706418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 26 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13A_ACTGAT_L008 sequencing assay ERX1825507 13A_ACTGAT_L008_1.fq.gz 13A_ACTGAT_L008_1.fq.gz ERR1758993 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758993/ERR1758993_1.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 4.5 hour +Sample 26 ERS1473723 SAMEA26706418 Crassostrea gigas Alexandrium minutum gill organism part P-MTAB-53255 P-MTAB-53256 P-MTAB-53257 Sample 26 RNA PAIRED PolyA TRANSCRIPTOMIC first strand RNA-Seq 345 7 5'-3'-3'-5' P-MTAB-53258 GeT-PlaGe Génopole Toulouse/Midi-pyrénées INRA Auzeville 24 Chemin de Borde Rouge-Auzeville CS52627 31326 Castanet-Tolosan FRANCE 13A_ACTGAT_L008 sequencing assay ERX1825507 13A_ACTGAT_L008_2.fq.gz 13A_ACTGAT_L008_2.fq.gz ERR1758993 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR175/003/ERR1758993/ERR1758993_2.fastq.gz 200 101 Alexandrium minutum Day 3 ZT 4.5 hour diff --git a/data/studies/PAYTON2017_HAB_AMINUTUM/ena_provenance.json b/data/studies/PAYTON2017_HAB_AMINUTUM/ena_provenance.json new file mode 100644 index 0000000..3820264 --- /dev/null +++ b/data/studies/PAYTON2017_HAB_AMINUTUM/ena_provenance.json @@ -0,0 +1,89 @@ +{ + "study_id": "PAYTON2017_HAB_AMINUTUM", + "bioproject": "PRJEB18614", + "date_generated": "2026-10-11", + "generated_by": "src/intake/ena_samplesheet.py", + "queries": { + "run_report": 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growth_condition organism_part library_layout instrument_model read_count +ERR1758942 ERR1758942 SAMEA26687668 E-MTAB-5345:Sample 16 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 30345012 +ERR1758943 ERR1758943 SAMEA26687668 E-MTAB-5345:Sample 16 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 30166434 +ERR1758944 ERR1758944 SAMEA26688418 E-MTAB-5345:Sample 3 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 32420669 +ERR1758945 ERR1758945 SAMEA26688418 E-MTAB-5345:Sample 3 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 32578173 +ERR1758946 ERR1758946 SAMEA26689168 E-MTAB-5345:Sample 17 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 25558853 +ERR1758947 ERR1758947 SAMEA26689168 E-MTAB-5345:Sample 17 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 25745506 +ERR1758948 ERR1758948 SAMEA26689918 E-MTAB-5345:Sample 4 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 34141980 +ERR1758949 ERR1758949 SAMEA26689918 E-MTAB-5345:Sample 4 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 34372878 +ERR1758950 ERR1758950 SAMEA26690668 E-MTAB-5345:Sample 18 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 35300496 +ERR1758951 ERR1758951 SAMEA26690668 E-MTAB-5345:Sample 18 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 35519670 +ERR1758952 ERR1758952 SAMEA26691418 E-MTAB-5345:Sample 5 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 29493129 +ERR1758953 ERR1758953 SAMEA26691418 E-MTAB-5345:Sample 5 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 29703862 +ERR1758954 ERR1758954 SAMEA26692168 E-MTAB-5345:Sample 1 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 31240302 +ERR1758955 ERR1758955 SAMEA26692168 E-MTAB-5345:Sample 1 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 31392744 +ERR1758956 ERR1758956 SAMEA26692918 E-MTAB-5345:Sample 14 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 43916668 +ERR1758957 ERR1758957 SAMEA26692918 E-MTAB-5345:Sample 14 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 43691832 +ERR1758958 ERR1758958 SAMEA26693668 E-MTAB-5345:Sample 15 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 30749516 +ERR1758959 ERR1758959 SAMEA26693668 E-MTAB-5345:Sample 15 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 30471628 +ERR1758960 ERR1758960 SAMEA26694418 E-MTAB-5345:Sample 2 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 33452383 +ERR1758961 ERR1758961 SAMEA26694418 E-MTAB-5345:Sample 2 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 33621449 +ERR1758962 ERR1758962 SAMEA26695168 E-MTAB-5345:Sample 19 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 35422253 +ERR1758963 ERR1758963 SAMEA26695168 E-MTAB-5345:Sample 19 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 35587637 +ERR1758964 ERR1758964 SAMEA26695918 E-MTAB-5345:Sample 6 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 29409020 +ERR1758965 ERR1758965 SAMEA26695918 E-MTAB-5345:Sample 6 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 29637879 +ERR1758966 ERR1758966 SAMEA26696668 E-MTAB-5345:Sample 22 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 31851724 +ERR1758967 ERR1758967 SAMEA26696668 E-MTAB-5345:Sample 22 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 31577868 +ERR1758968 ERR1758968 SAMEA26697418 E-MTAB-5345:Sample 9 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 31028684 +ERR1758969 ERR1758969 SAMEA26697418 E-MTAB-5345:Sample 9 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 31245763 +ERR1758970 ERR1758970 SAMEA26698168 E-MTAB-5345:Sample 10 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 23409198 +ERR1758971 ERR1758971 SAMEA26698168 E-MTAB-5345:Sample 10 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 23548761 +ERR1758972 ERR1758972 SAMEA26698918 E-MTAB-5345:Sample 23 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 30282250 +ERR1758973 ERR1758973 SAMEA26698918 E-MTAB-5345:Sample 23 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 30693329 +ERR1758974 ERR1758974 SAMEA26699668 E-MTAB-5345:Sample 11 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 36689534 +ERR1758975 ERR1758975 SAMEA26699668 E-MTAB-5345:Sample 11 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 37207467 +ERR1758976 ERR1758976 SAMEA26700418 E-MTAB-5345:Sample 24 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 33187997 +ERR1758977 ERR1758977 SAMEA26700418 E-MTAB-5345:Sample 24 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 33640079 +ERR1758978 ERR1758978 SAMEA26701168 E-MTAB-5345:Sample 20 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 31333534 +ERR1758979 ERR1758979 SAMEA26701168 E-MTAB-5345:Sample 20 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 31037326 +ERR1758980 ERR1758980 SAMEA26701918 E-MTAB-5345:Sample 7 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 34834025 +ERR1758981 ERR1758981 SAMEA26701918 E-MTAB-5345:Sample 7 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 34586737 +ERR1758982 ERR1758982 SAMEA26702668 E-MTAB-5345:Sample 21 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 33155799 +ERR1758983 ERR1758983 SAMEA26702668 E-MTAB-5345:Sample 21 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 32770696 +ERR1758984 ERR1758984 SAMEA26703418 E-MTAB-5345:Sample 8 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 31283316 +ERR1758985 ERR1758985 SAMEA26703418 E-MTAB-5345:Sample 8 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 31535582 +ERR1758986 ERR1758986 SAMEA26704168 E-MTAB-5345:Sample 12 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 27294388 +ERR1758987 ERR1758987 SAMEA26704168 E-MTAB-5345:Sample 12 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 27638408 +ERR1758988 ERR1758988 SAMEA26704918 E-MTAB-5345:Sample 25 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 30911964 +ERR1758989 ERR1758989 SAMEA26704918 E-MTAB-5345:Sample 25 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 31342608 +ERR1758990 ERR1758990 SAMEA26705668 E-MTAB-5345:Sample 13 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 25663769 +ERR1758991 ERR1758991 SAMEA26705668 E-MTAB-5345:Sample 13 Heterocapsa_triquetra Heterocapsa triquetra gill PAIRED Illumina HiSeq 2500 26038942 +ERR1758992 ERR1758992 SAMEA26706418 E-MTAB-5345:Sample 26 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 27363885 +ERR1758993 ERR1758993 SAMEA26706418 E-MTAB-5345:Sample 26 Alexandrium_minutum Alexandrium minutum gill PAIRED Illumina HiSeq 2500 27766300 diff --git a/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml b/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml index 6cd3800..a476aa0 100644 --- a/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml +++ b/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml @@ -1,62 +1,124 @@ -# Copy this file to registry/studies/.yaml and fill in every field. -# Validate with: aree validate-study registry/studies/.yaml -# See docs/adding_a_study.md for field-by-field guidance. +# Harmful algal bloom exposure: adult gill after 6 days on the paralytic- +# shellfish-toxin (PST) producer Alexandrium minutum vs a non-toxic +# dinoflagellate. AREE's FIRST harmful_algal_bloom STRESSOR. Chosen +# 2026-10-11 from the RNA-seq studies the sister repository sr320/AREE-co had +# curated; not in candidate_studies.md. +# +# Source: Payton et al. 2017, Sci Rep (open access, PMC5471176); data +# ArrayExpress E-MTAB-5345 = ENA PRJEB18614. Methods read in full 2026-10-11. +# The paper's subject is the circadian transcriptome; AREE uses only its +# diet contrast, as the paper's own differential-expression analysis did +# ("considering the 13 sample times ... of each algal treatment as +# replicates"). +# +# REPLICATION, AND ITS LIMIT. 156 oysters in six tanks, three per diet. During +# the last two days, gill of six oysters per diet was taken every 4 h for +# 52 h and pooled per diet and time: 13 libraries per diet, each pooling +# animals from that diet's three tanks, each sequenced on two lanes. So the +# replicates DESeq2 sees are the 13 libraries (lanes summed with +# replicate_unit = sample_accession), which are different animals at +# different times of day. Every library contains the same three tanks, so +# tank-to-tank variation never enters the error term: lfcSE is somewhat too +# small, in the way LUTIER2022's would have been without pseudo-bulking. The +# libraries cannot be assigned to tanks, so this cannot be fixed; it is +# flagged (tank_level_replication) and limits how much weight the study +# should carry. Time-of-day is balanced between diets but not modelled. +# +# PHENOTYPE. Exposure is confirmed (gill PST 95.8 ± 13.5 ng STX eq/g in the +# A. minutum group, none in controls) and valve behaviour changed (daytime +# valve-opening rose from 20.6% to 38.0%), but no tolerance outcome was +# measured. So toxicant_tolerance is the axis and the comparison is +# stress_response, overriding the ontology default. study_id: PAYTON2017_HAB_AMINUTUM simulated: false accessions: - doi: null + doi: "10.1038/s41598-017-03797-4" bioproject: "PRJEB18614" geo: null - sra: null - ena: null + sra: "ERR1758942-ERR1758993" + ena: "PRJEB18614" proteomexchange: null - other: null + other: "ArrayExpress E-MTAB-5345; BioSamples ERS1473698-ERS1473723; PMID 28615697; PMC5471176" -citation: "Author A, Author B (YEAR). Title. Journal. https://doi.org/..." -species: "Crassostrea gigas" -strain_or_population: null -genome_assembly: "cgigas_uk_roslin_v1" -annotation_version: null +citation: "Payton L, Perrigault M, Hoede C, Massabuau JC, Sow M, Huvet A, Boullot F, Fabioux C, Hegaret H, Tran D (2017). Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum. Scientific Reports 7:3480. https://doi.org/10.1038/s41598-017-03797-4" + +species: "Magallana gigas" +strain_or_population: "Diploid oysters, 1.5 years old, Bay of Arcachon, France (72.8 ± 0.5 mm shell length); held at 15 C, 9 h light : 15 h dark, in December to avoid gametogenesis." + +genome_assembly: "GCF_963853765.1" +annotation_version: "GCF_963853765.1-RS_2024_06" assay_type: ["rnaseq"] -analysis_mode: "processed_results_harmonization" # or raw_reanalysis -platform: null +analysis_mode: "raw_reanalysis" +platform: "Illumina HiSeq 2500, paired-end 100 bp, TruSeq Stranded mRNA; 26 pooled libraries, each on two lanes (52 runs, 23.4-43.9 M read pairs per run; 274 GB FASTQ reported by ENA)" data_availability: - raw_data_available: false - processed_data_available: true - status: "available" # available | restricted | embargoed | unavailable - access_notes: null + raw_data_available: true + processed_data_available: false + status: "available" + access_notes: "Raw paired-end FASTQ for all 52 runs are public in ENA (PRJEB18614) / ArrayExpress (E-MTAB-5345). Diet is the ENA sample attribute `growth condition`; sampling time is only in the ArrayExpress SDRF, committed here as E-MTAB-5345.sdrf.txt. Sequence data are not committed." -qc_status: "not_started" -analysis_status: "not_started" +qc_status: "in_progress" +analysis_status: "in_progress" comparisons: - - comparison_id: "comp1" + - comparison_id: "alexandrium_vs_heterocapsa_6d" tissue: "gill" life_stage: "adult" - stressor_original: "exact wording from the source paper" - stressor_standardized: "temperature" - exposure_intensity: null - exposure_duration: null - exposure_timing: null - control_condition: "describe control arm" - treatment_condition: "describe treatment arm" - phenotype: "thermal_tolerance" - phenotype_direction: "decrease" + stressor_original: "Continuous feeding on the PST-producing dinoflagellate Alexandrium minutum (strain AM89BM), ~400 cells/mL in tanks, 'mimicking a realistic HAB', for 6 days; control fed the non-toxic dinoflagellate Heterocapsa triquetra (strain HT99PZ) at matched supply (Payton et al. 2017); ENA growth condition 'Alexandrium minutum' / 'Heterocapsa triquetra'" + stressor_standardized: "harmful_algal_bloom" + exposure_intensity: "A. minutum 430.9 ± 160.8 cells/mL measured in tanks (1.3 pg saxitoxin per cell), vs H. triquetra 159.1 ± 15.7 cells/mL; gill PST burden 95.8 ± 13.5 ng STX eq/g" + exposure_duration: "6 days; gill sampled during the last 52 h" + exposure_timing: "sampled every 4 h over 52 h (13 times, Zeitgeber time) on days 5-6 of exposure; times pooled as replicates" + control_condition: "Heterocapsa triquetra (non-toxic dinoflagellate) diet; 3 tanks; 13 pooled libraries (6 oysters each), one per sampling time" + treatment_condition: "Alexandrium minutum (PST-producing) diet; 3 tanks; 13 pooled libraries (6 oysters each), one per sampling time" + phenotype: "toxicant_tolerance" + phenotype_direction: "not_applicable" phenotype_unit: null - resilience_classification: "resilience" - sample_size: 0 - biological_replicates: 0 + resilience_classification: "stress_response" + sample_size: 26 + biological_replicates: 13 + meta_analysis_primary: true results_file: null -quality_flags: [] -limitations: null +quality_flags: + - raw_data_available + - tank_level_replication # each library pools a diet's three tanks; tank variance is absent from lfcSE + +limitations: > + (1) Treatment was applied per tank (three per diet), but every library + pools animals from all three tanks of its diet, so tank-to-tank variation is + not in the error term and lfcSE is somewhat anti-conservative; the 13 + libraries per diet differ in animals and time of day, not tank. (2) + Libraries pool six oysters. (3) Sampling times are pooled as replicates; + circadian variation, which the paper shows is large and is itself changed + by A. minutum, adds variance and can make a time-specific effect look + smaller. (4) No tolerance outcome was measured: the comparison describes + the response to a realistic toxic bloom, not which oysters cope with it. + (5) The control alga differs from A. minutum in more than toxicity, and + its measured density in tanks was lower. provenance: registered_by: "sr320" date_registered: "2026-10-11" - curation_notes: null - source_links: [] + curation_notes: > + Claimed with `aree start-study --accession PRJEB18614 --study-id + PAYTON2017_HAB_AMINUTUM` (draft PR sr320/AREE#32). Uses the + toxicant_tolerance phenotype added by sr320/AREE#31; this branch contains + that commit until #31 merges. Sample sheet from live ENA metadata with + `aree fetch-samplesheet --label-field run_accession` (each run its own + sample_id) and `--condition-attribute "growth condition"`: 52 runs, 26 per + diet, two runs per BioSample, which are the two sequencing lanes of one + pooled library (paper methods). replicate_unit = sample_accession sums the + lanes. All 26 libraries are used, as in the paper's own DE analysis (an + earlier reanalysis in sr320/AREE-co dropped both day-2 ZT 8.5 pools by its + own QC rule; AREE does not, without an author-stated reason). + meta_analysis_primary is set on the study's only comparison; there is no + other real HAB study to pool with yet. + source_links: + - "https://doi.org/10.1038/s41598-017-03797-4" + - "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471176/" + - "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-5345" + - "https://www.ebi.ac.uk/ena/browser/view/PRJEB18614" diff --git a/tests/test_payton2017_hab_study.py b/tests/test_payton2017_hab_study.py new file mode 100644 index 0000000..560bc6b --- /dev/null +++ b/tests/test_payton2017_hab_study.py @@ -0,0 +1,95 @@ +"""Curation tests for PAYTON2017_HAB_AMINUTUM. + +Payton et al. 2017 (PRJEB18614 / E-MTAB-5345): adult gill after 6 days on +the toxic dinoflagellate Alexandrium minutum vs non-toxic Heterocapsa +triquetra, 13 pooled libraries per diet (one per sampling time), each on two +lanes. AREE's first harmful-algal-bloom study. These tests pin the diet +labels against the ArrayExpress SDRF, the lane structure (two runs per +library, summed by replicate_unit), and the classification. +""" +from __future__ import annotations + +import csv +import json +import re +from collections import Counter, defaultdict + +import pytest +import yaml + +from common import DATA_DIR, REPO_ROOT, STUDIES_DIR + +STUDY_PATH = STUDIES_DIR / "PAYTON2017_HAB_AMINUTUM.yaml" +STUDY_DIR = DATA_DIR / "studies" / "PAYTON2017_HAB_AMINUTUM" +CONFIG = REPO_ROOT / "config" / "PAYTON2017_HAB_AMINUTUM.config" + + +def _tsv(path): + with open(path, newline="") as fh: + return list(csv.DictReader(fh, delimiter="\t")) + + +@pytest.fixture(scope="module") +def study(): + return yaml.safe_load(STUDY_PATH.read_text()) + + +@pytest.fixture(scope="module") +def samplesheet(): + return _tsv(STUDY_DIR / "samplesheet.tsv") + + +@pytest.fixture(scope="module") +def sdrf_by_run(): + rows = _tsv(STUDY_DIR / "E-MTAB-5345.sdrf.txt") + return {r["Comment[ENA_RUN]"]: r for r in rows} + + +def test_study_validates(): + from intake.schema_validate import validate_study_file + + result = validate_study_file(STUDY_PATH) + assert result.valid, result.errors + + +def test_diet_matches_the_arrayexpress_sdrf_for_every_run(samplesheet, sdrf_by_run): + assert set(sdrf_by_run) == {r["run_accession"] for r in samplesheet} + for row in samplesheet: + assert row["growth_condition"] == sdrf_by_run[row["run_accession"]]["Factor Value[feeding condition]"] + + +def test_two_lanes_per_library_thirteen_libraries_per_diet(samplesheet, sdrf_by_run): + runs_per_library = Counter(r["sample_accession"] for r in samplesheet) + assert set(runs_per_library.values()) == {2} + libraries = defaultdict(set) + times = defaultdict(set) + for row in samplesheet: + libraries[row["condition"]].add(row["sample_accession"]) + times[row["condition"]].add(sdrf_by_run[row["run_accession"]]["Factor Value[time]"]) + assert {k: len(v) for k, v in libraries.items()} == {"Alexandrium_minutum": 13, "Heterocapsa_triquetra": 13} + # Time-matched: both diets sampled at the same 13 times. + assert times["Alexandrium_minutum"] == times["Heterocapsa_triquetra"] + assert len(times["Alexandrium_minutum"]) == 13 + + +def test_lanes_are_summed_so_libraries_are_the_replicates(study): + assert re.search(r"replicate_unit\s*=\s*'sample_accession'", CONFIG.read_text()) + (comp,) = study["comparisons"] + assert comp["biological_replicates"] == 13 and comp["sample_size"] == 26 + + +def test_hab_exposure_is_stress_response_with_its_replication_caveat(study): + (comp,) = study["comparisons"] + assert comp["stressor_standardized"] == "harmful_algal_bloom" + assert comp["phenotype"] == "toxicant_tolerance" + assert comp["resilience_classification"] == "stress_response" + assert comp["meta_analysis_primary"] is True + assert "tank_level_replication" in study["quality_flags"] + + +def test_provenance_and_manifest(samplesheet): + prov = json.loads((STUDY_DIR / "ena_provenance.json").read_text()) + assert prov["bioproject"] == "PRJEB18614" and prov["n_runs"] == 52 + manifest = _tsv(STUDY_DIR / "fastq_manifest.tsv") + assert len(manifest) == 104 + assert all(len(r["md5"]) == 32 for r in manifest) From 87012c1a70e2122c5382f3ccd81e56f0518c3586 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Mon, 12 Oct 2026 07:54:00 -0700 Subject: [PATCH 3/4] Rename curation test to tests/test_payton2017_hab_aminutum.py, as check-study-scope requires Co-Authored-By: Claude Opus 5.5 --- ...st_payton2017_hab_study.py => test_payton2017_hab_aminutum.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename tests/{test_payton2017_hab_study.py => test_payton2017_hab_aminutum.py} (100%) diff --git a/tests/test_payton2017_hab_study.py b/tests/test_payton2017_hab_aminutum.py similarity index 100% rename from tests/test_payton2017_hab_study.py rename to tests/test_payton2017_hab_aminutum.py From 7ddcfb09882e1a898e8229e471f25bdf25934f41 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Sat, 17 Oct 2026 14:06:39 -0700 Subject: [PATCH 4/4] PAYTON2017_HAB_AMINUTUM: merge as a registration with the run pending The RNA-seq run was never done; set qc_status and analysis_status from in_progress to not_started, say so in the YAML, and pin it in a test. Co-Authored-By: Claude Opus 5.5 --- registry/studies/PAYTON2017_HAB_AMINUTUM.yaml | 14 +++++++++++--- tests/test_payton2017_hab_aminutum.py | 6 ++++++ 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml b/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml index a476aa0..b11a11d 100644 --- a/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml +++ b/registry/studies/PAYTON2017_HAB_AMINUTUM.yaml @@ -29,6 +29,12 @@ # valve-opening rose from 20.6% to 38.0%), but no tolerance outcome was # measured. So toxicant_tolerance is the axis and the comparison is # stress_response, overriding the ontology default. +# +# MERGED AS A REGISTRATION (2026-10-17), RUN PENDING. The sample sheet, FASTQ +# manifest and run configuration are ready, but the RNA-seq workflow has not +# been run: no results, manifests or reports are committed, results_file is +# null, and both status fields are not_started. Run it in a follow-up study +# PR from a fresh `aree start-study`-style branch. study_id: PAYTON2017_HAB_AMINUTUM simulated: false @@ -60,8 +66,8 @@ data_availability: status: "available" access_notes: "Raw paired-end FASTQ for all 52 runs are public in ENA (PRJEB18614) / ArrayExpress (E-MTAB-5345). Diet is the ENA sample attribute `growth condition`; sampling time is only in the ArrayExpress SDRF, committed here as E-MTAB-5345.sdrf.txt. Sequence data are not committed." -qc_status: "in_progress" -analysis_status: "in_progress" +qc_status: "not_started" +analysis_status: "not_started" comparisons: - comparison_id: "alexandrium_vs_heterocapsa_6d" @@ -116,7 +122,9 @@ provenance: earlier reanalysis in sr320/AREE-co dropped both day-2 ZT 8.5 pools by its own QC rule; AREE does not, without an author-stated reason). meta_analysis_primary is set on the study's only comparison; there is no - other real HAB study to pool with yet. + other real HAB study to pool with yet. 2026-10-17: merged as a + registration with the run pending (status fields set from in_progress to + not_started, since no run is under way). source_links: - "https://doi.org/10.1038/s41598-017-03797-4" - "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471176/" diff --git a/tests/test_payton2017_hab_aminutum.py b/tests/test_payton2017_hab_aminutum.py index 560bc6b..7518a7a 100644 --- a/tests/test_payton2017_hab_aminutum.py +++ b/tests/test_payton2017_hab_aminutum.py @@ -93,3 +93,9 @@ def test_provenance_and_manifest(samplesheet): manifest = _tsv(STUDY_DIR / "fastq_manifest.tsv") assert len(manifest) == 104 assert all(len(r["md5"]) == 32 for r in manifest) + + +def test_merged_as_a_registration_with_the_run_pending(): + study = yaml.safe_load((STUDIES_DIR / "PAYTON2017_HAB_AMINUTUM.yaml").read_text()) + assert study["qc_status"] == "not_started" and study["analysis_status"] == "not_started" + assert all(c["results_file"] is None for c in study["comparisons"])