[study] LIU2019_HEAT_HSF1 (PRJNA516762)

config/LIU2019_HEAT_HSF1.config

@@ -0,0 +1,59 @@
+/*
+ * AREE :: run configuration for LIU2019_HEAT_HSF1 (PRJNA516762)
+ *
+ * Liu et al. 2019, BMC Genomics 20:639 (doi:10.1186/s12864-019-6003-8).
+ * 7-month-old oysters, gill; heat shock at 35 C for 2 h vs untreated control,
+ * three pooled libraries (five oysters each) per group. The deposit also has
+ * HSF1-RNAi and RNAi + heat groups; only the direct heat-vs-control contrast
+ * is used, and only its six runs are staged.
+ *
+ *   nextflow run workflows/rnaseq -config config/LIU2019_HEAT_HSF1.config \
+ *     -profile local,workstation
+ *
+ *   aree fetch-samplesheet --bioproject PRJNA516762 --study LIU2019_HEAT_HSF1 \
+ *     --label-field sample_alias \
+ *     --label-pattern '^(?P<treatment>control|HS&RNAi|HS|RNAi)-(?P<replicate>[1-3])$' \
+ *     --condition-attribute treatment --attribute replicate --attribute tissue \
+ *     --attribute dev_stage --attribute isolation_source
+ */
+
+includeConfig 'base.config'
+
+params {
+    mode = 'raw_reanalysis'
+
+    rnaseq {
+        study_id           = 'LIU2019_HEAT_HSF1'
+        // 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 = 'heat_35c_2h_vs_control'
+
+    sample_sheet = 'data/studies/LIU2019_HEAT_HSF1/samplesheet.tsv'
+
+    control_level   = 'control'
+    treatment_level = 'HS'
+
+    // The six control and HS runs (19 GB), already staged on this machine
+    // from an earlier pass and verified against ENA's MD5s on 2026-10-12.
+    reads = 'data/raw/LIU2019_HEAT_HSF1/SRR*_{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/LIU2019_HEAT_HSF1'
+}
+
+process {
+    // 6 HiSeq X Ten 2x150 libraries, 22.2-31.9 M read pairs. 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'  }
+}

data/studies/LIU2019_HEAT_HSF1/LIU2019_HEAT_HSF1_heat_35c_2h_vs_control_workflow_manifest.json

@@ -0,0 +1,85 @@
+{
+  "workflow_name": "aree-rnaseq",
+  "workflow_version": "0.1.0-scaffold",
+  "mode": "raw_reanalysis",
+  "study_id": "LIU2019_HEAT_HSF1",
+  "comparison_id": "heat_35c_2h_vs_control",
+  "input_files": [
+    {
+      "name": "LIU2019_HEAT_HSF1_heat_35c_2h_vs_control_dge_standardized.tsv",
+      "sha256": "11ace864f83be527d7ee1ca857b1fd092577fc71ab23f3e6958f88da89b5764d"
+    }
+  ],
+  "parameters": {
+    "mode": "raw_reanalysis",
+    "study_id": "LIU2019_HEAT_HSF1",
+    "comparison_id": "heat_35c_2h_vs_control",
+    "outdir": "results/rnaseq/LIU2019_HEAT_HSF1",
+    "exclude_samples": [],
+    "control_levels": [
+      "control"
+    ],
+    "treatment_levels": [
+      "HS"
+    ],
+    "replicate_unit": null,
+    "covariates": [],
+    "single_end": false,
+    "se_adapter": null,
+    "viral_reference": null
+  },
+  "deseq2_design": {
+    "design": "~condition",
+    "covariates_requested": [],
+    "covariates_used": [],
+    "covariates_dropped_constant": [],
+    "n_libraries_or_units": 6,
+    "residual_df": 4
+  },
+  "software_versions": {
+    "DIFFERENTIAL_EXPRESSION_DESEQ2": {
+      "bioconductor-deseq2": "1.42.1",
+      "bioconductor-tximport": "1.30.0",
+      "r-base": "4.3.2"
+    },
+    "FASTQC": {
+      "fastqc": "0.12.1"
+    },
+    "SALMON_INDEX": {
+      "salmon": "2.3.4"
+    },
+    "SALMON_QUANT": {
+      "salmon": "2.3.4"
+    },
+    "SAMPLE_QC": {
+      "multiqc": "1.9"
+    },
+    "STANDARDIZE_OUTPUT": {
+      "pandas": "2.3.3",
+      "python": "3.9.6"
+    },
+    "TRIM_FASTP": {
+      "fastp": "1.3.6"
+    },
+    "EMIT_MANIFEST": {
+      "python": "3.9.6"
+    }
+  },
+  "software_versions_not_captured": {
+    "RENDER_REPORT": "renders this manifest, so it runs afterwards; its versions.yml is published to rnaseq/reports/"
+  },
+  "container_engine": null,
+  "reference": {
+    "genome_assembly": "GCF_963853765.1",
+    "annotation_version": "GCF_963853765.1-RS_2024_06"
+  },
+  "workflow_start": "2026-10-12T06:21:09.692598-07:00",
+  "qc_metrics": {
+    "mean_reads_per_sample": null,
+    "mean_mapping_rate_percent": null,
+    "n_samples": null,
+    "note": "QC metrics are not populated in processed_results_harmonization mode or in this unexecuted scaffold run."
+  },
+  "viral_load": null,
+  "warnings": []
+}

data/studies/LIU2019_HEAT_HSF1/ena_provenance.json

@@ -0,0 +1,51 @@
+{
+  "study_id": "LIU2019_HEAT_HSF1",
+  "bioproject": "PRJNA516762",
+  "date_generated": "2026-10-12",
+  "generated_by": "src/intake/ena_samplesheet.py",
+  "queries": {
+    "run_report": "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA516762&result=read_run&fields=run_accession,sample_accession,sample_alias,experiment_accession,library_strategy,library_layout,library_selection,instrument_model,read_count,base_count,fastq_ftp,fastq_md5,fastq_bytes",
+    "sample_xml": "https://www.ebi.ac.uk/ena/browser/api/xml/<sample_accessions>"
+  },
+  "condition_attributes": [
+    "treatment"
+  ],
+  "n_runs": 12,
+  "n_samples": 12,
+  "library_strategies": [
+    "RNA-Seq"
+  ],
+  "library_layouts": [
+    "PAIRED"
+  ],
+  "group_sizes": {
+    "HS": 3,
+    "HS_RNAi": 3,
+    "RNAi": 3,
+    "control": 3
+  },
+  "min_group_size": 3,
+  "total_fastq_bytes": 40948854116,
+  "outputs": {
+    "data/studies/LIU2019_HEAT_HSF1/samplesheet.tsv": "863737966d8e476fe08a48f5a04ef8246200ce547c32507a8cdddc82839d9481",
+    "data/studies/LIU2019_HEAT_HSF1/fastq_manifest.tsv": "fd01ff72951f8c10189c40280ae243e8e38e0248bbc9372da15997a72eeb0183"
+  },
+  "run_labels": {
+    "field": "sample_alias",
+    "pattern": "^(?P<treatment>control|HS&RNAi|HS|RNAi)-(?P<replicate>[1-3])$",
+    "labels": {
+      "SRR8485503": "HS&RNAi-2",
+      "SRR8485504": "HS&RNAi-3",
+      "SRR8485505": "RNAi-1",
+      "SRR8485506": "RNAi-2",
+      "SRR8485507": "HS-2",
+      "SRR8485508": "HS-3",
+      "SRR8485509": "control-3",
+      "SRR8485510": "HS-1",
+      "SRR8485511": "control-1",
+      "SRR8485512": "control-2",
+      "SRR8485513": "RNAi-3",
+      "SRR8485514": "HS&RNAi-1"
+    }
+  }
+}

data/studies/LIU2019_HEAT_HSF1/fastq_manifest.tsv

@@ -0,0 +1,25 @@
+run_accession	mate	url	md5	bytes
+SRR8485503	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/003/SRR8485503/SRR8485503_1.fastq.gz	61a8b41dd02ca98b5efe9fde67d956e4	2175708430
+SRR8485503	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/003/SRR8485503/SRR8485503_2.fastq.gz	203a3b606de51bb588dee115c173fd9f	2258551162
+SRR8485504	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/004/SRR8485504/SRR8485504_1.fastq.gz	0a11df86e2cddec4951cbae7986a460e	1770042099
+SRR8485504	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/004/SRR8485504/SRR8485504_2.fastq.gz	fbd6402d85f60a2bff065f03a94b1307	1830327507
+SRR8485505	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/005/SRR8485505/SRR8485505_1.fastq.gz	a3f30ca97e135921ab771e38b71f1425	1547272101
+SRR8485505	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/005/SRR8485505/SRR8485505_2.fastq.gz	6d7ba41612d871bff3b7d6a3a8788022	1577157364
+SRR8485506	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/006/SRR8485506/SRR8485506_1.fastq.gz	fb1a760d4dfea175e5612fc4c4eb9537	1382386685
+SRR8485506	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/006/SRR8485506/SRR8485506_2.fastq.gz	68d0c10b19cd385751983db301faae33	1437516366
+SRR8485507	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/007/SRR8485507/SRR8485507_1.fastq.gz	c9b80db0a6ab13bf3417f586decc38ea	1592999519
+SRR8485507	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/007/SRR8485507/SRR8485507_2.fastq.gz	f0c959e8473816c1dc76d94405c247df	1684740929
+SRR8485508	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/008/SRR8485508/SRR8485508_1.fastq.gz	6fabdc943e9c336bf88f77f094a17adc	1518419757
+SRR8485508	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/008/SRR8485508/SRR8485508_2.fastq.gz	fd5262f9023732b8d5dc4503e95423eb	1573757704
+SRR8485509	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/009/SRR8485509/SRR8485509_1.fastq.gz	1d53fa017b358ab5a496c17e68806079	1553193079
+SRR8485509	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/009/SRR8485509/SRR8485509_2.fastq.gz	e21820b8aa2d1254abaa1ffe167a133c	1614426587
+SRR8485510	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/000/SRR8485510/SRR8485510_1.fastq.gz	7d87c9d50ab70ff3d92d2b59ab0daa32	1679158321
+SRR8485510	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/000/SRR8485510/SRR8485510_2.fastq.gz	ee954cce54d6b1fd685bf53f60f02993	1737612939
+SRR8485511	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/001/SRR8485511/SRR8485511_1.fastq.gz	bc108fe40953d8409ee1e84ccd47657e	1388005940
+SRR8485511	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/001/SRR8485511/SRR8485511_2.fastq.gz	d6adf82b3eb226883eeec9c03be4b2ce	1416959264
+SRR8485512	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/002/SRR8485512/SRR8485512_1.fastq.gz	76ff5590ff13ef5aee56120caa935903	2020757429
+SRR8485512	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/002/SRR8485512/SRR8485512_2.fastq.gz	c86eaf22e336e040df0b5e0a65201ccb	2072887209
+SRR8485513	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/003/SRR8485513/SRR8485513_1.fastq.gz	c219a8dd56257b22f12696c9313b801d	1888989814
+SRR8485513	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/003/SRR8485513/SRR8485513_2.fastq.gz	b5926b5411c2e33e7fcb0395eafc8397	1954486468
+SRR8485514	1	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/004/SRR8485514/SRR8485514_1.fastq.gz	678a7e2f55d1fa17421763be78474808	1606421827
+SRR8485514	2	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR848/004/SRR8485514/SRR8485514_2.fastq.gz	ef256ae03ca6a85acaee788d041e961c	1667075616

data/studies/LIU2019_HEAT_HSF1/replicate_dispersion_qc.tsv

@@ -0,0 +1,3 @@
+condition	n_samples	samples	n_genes	median_dispersion	passes
+HS	3	HS-1,HS-2,HS-3	7321	0.00772	True
+control	3	control-1,control-2,control-3	7371	0.00494	False

data/studies/LIU2019_HEAT_HSF1/replicate_genotype_check.txt

@@ -0,0 +1,14 @@
+# Expressed-SNP replicate check, 2026-10-12: scripts/check_replicate_genotypes.py from sr320/AREE-co
+# (targets -> pileup of the first 4M read pairs per library through Salmon --writeMappings -> compare).
+# Library names: control_1..3 = SRR8485511, SRR8485512, SRR8485509; HS_1..3 = SRR8485510, SRR8485507, SRR8485508.
+3244 sites with pooled minor-allele frequency >= 0.15 and depth >= 30 in all 6 libraries
+per-library allele-frequency histogram (0-1 in tenths); one diploid animal peaks at 0, 0.5 and 1:
+  control_1            [461 604 718 600 377 270 130  62  17   5]
+  control_2            [510 594 693 562 401 256 145  51  25   7]
+  control_3            [494 597 661 539 419 305 133  57  28  11]
+  HS_1                 [480 620 662 581 414 271 128  62  19   7]
+  HS_2                 [472 567 714 586 428 270 126  53  22   6]
+  HS_3                 [487 577 678 583 414 292 131  62  13   7]
+mean |allele-frequency difference| (observed, same-RNA simulation, correlation):
+  within   pairs=  6 observed 0.188 (0.185-0.192) noise 0.054 r 0.17
+  between  pairs=  9 observed 0.187 (0.182-0.192) noise 0.054 r 0.17

data/studies/LIU2019_HEAT_HSF1/samplesheet.tsv

@@ -0,0 +1,13 @@
+sample_id	run_accession	sample_accession	sample_alias	condition	treatment	replicate	tissue	dev_stage	isolation_source	library_layout	instrument_model	read_count
+HS&RNAi-2	SRR8485503	SAMN10797492	HS&RNAi-2	HS_RNAi	HS&RNAi	2	Gill			PAIRED	HiSeq X Ten	34629649
+HS&RNAi-3	SRR8485504	SAMN10797493	HS&RNAi-3	HS_RNAi	HS&RNAi	3	Gill			PAIRED	HiSeq X Ten	27967779
+RNAi-1	SRR8485505	SAMN10797488	RNAi-1	RNAi	RNAi	1	Gill			PAIRED	HiSeq X Ten	22315653
+RNAi-2	SRR8485506	SAMN10797489	RNAi-2	RNAi	RNAi	2	Gill			PAIRED	HiSeq X Ten	21939922
+HS-2	SRR8485507	SAMN10797486	HS-2	HS	HS	2	Gill			PAIRED	HiSeq X Ten	25256450
+HS-3	SRR8485508	SAMN10797487	HS-3	HS	HS	3	Gill			PAIRED	HiSeq X Ten	24141499
+control-3	SRR8485509	SAMN10797484	control-3	control	control	3	Gill			PAIRED	HiSeq X Ten	24704556
+HS-1	SRR8485510	SAMN10797485	HS-1	HS	HS	1	Gill			PAIRED	HiSeq X Ten	26697058
+control-1	SRR8485511	SAMN10797482	control-1	control	control	1	Gill			PAIRED	HiSeq X Ten	22182168
+control-2	SRR8485512	SAMN10797483	control-2	control	control	2	Gill			PAIRED	HiSeq X Ten	31879314
+RNAi-3	SRR8485513	SAMN10797490	RNAi-3	RNAi	RNAi	3	Gill			PAIRED	HiSeq X Ten	27724593
+HS&RNAi-1	SRR8485514	SAMN10797491	HS&RNAi-1	HS_RNAi	HS&RNAi	1	Gill			PAIRED	HiSeq X Ten	25493469

registry/studies/LIU2019_HEAT_HSF1.yaml

@@ -0,0 +1,127 @@
+# Acute heat shock (35 C, 2 h) in gill of 7-month-old M. gigas. Chosen
+# 2026-10-12 because its six control and heat runs were already staged and
+# MD5-verified on this machine (from an earlier pass in sr320/AREE-co), so it
+# could use idle CPU while every other queued study waited on slow ENA
+# downloads; not in candidate_studies.md.
+#
+# Source: Liu et al. 2019, BMC Genomics (open access, PMC6688261). The paper
+# is about HSF1 (RNAi knockdown); AREE uses only its direct heat-shock vs
+# control contrast, which the paper also reports (group 2 vs group 1).
+#
+# REPLICATION. "15 individuals of each group (three replicates of five
+# individuals) were selected for RNA-seq": three pooled libraries per group,
+# five oysters each. Two caveats from the methods: (1) the animals were
+# selected "according to the analysis of HSF1 expression" (qRT-PCR) before
+# sequencing, so the sequenced oysters are not a random draw from the heated
+# group; (2) tanks are not described, and each treatment group appears to
+# have been held as one group, so the treatment may not be replicated at the
+# container level. Both limit the weight this study should carry.
+
+study_id: LIU2019_HEAT_HSF1
+simulated: false
+
+accessions:
+  doi: "10.1186/s12864-019-6003-8"
+  bioproject: "PRJNA516762"
+  geo: null
+  sra: "SRP181984; runs used SRR8485507-SRR8485512"
+  ena: "PRJNA516762"
+  proteomexchange: null
+  other: "PMID 31395030; PMC6688261"
+
+citation: "Liu Y, Li L, Huang B, Wang W, Zhang G (2019). RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress. BMC Genomics 20:639. https://doi.org/10.1186/s12864-019-6003-8"
+
+species: "Magallana gigas"
+strain_or_population: "7-month-old cultured oysters (58.6 ± 1.3 mm, 23.4 ± 1.6 g); acclimated 1 week at 12 ± 1 C. Population per the deposit's isolation_source."
+
+genome_assembly: "GCF_963853765.1"
+annotation_version: "GCF_963853765.1-RS_2024_06"
+
+assay_type: ["rnaseq"]
+analysis_mode: "raw_reanalysis"
+platform: "Illumina HiSeq X Ten, paired-end 150 bp, NEBNext Ultra (12 libraries deposited; the 6 control and heat-shock libraries used, 22.2-31.9 M read pairs)"
+
+data_availability:
+  raw_data_available: true
+  processed_data_available: false
+  status: "available"
+  access_notes: "Raw paired-end FASTQ for all 12 runs are public in ENA/SRA under PRJNA516762. Groups are in the sample alias (control-n, HS-n, RNAi-n, HS&RNAi-n). Only the six control and HS runs are staged and used. Sequence data are not committed."
+
+# QC PASSED WITH WARNINGS, 2026-10-12 (full-depth run of the 6 libraries).
+# - Dispersion was borderline: median within-group dispersion 0.0077 (HS) and
+#   0.00494 (control), the latter just under the 0.005 screening floor of
+#   scripts/check_replicate_dispersion.py. That floor is calibrated on
+#   single-animal libraries; each library here pools five oysters, which by
+#   itself cuts dispersion about fivefold (real single-animal replicates sit
+#   at 0.03-0.05, so ~0.006-0.01 is expected for pools of five).
+# - The genotype check settles it: an expressed-SNP comparison (3,244 sites)
+#   finds pools within a group differ in allele frequency by 0.188, against
+#   0.054 expected for one RNA sample sequenced twice, and exactly as much as
+#   pools from different groups (0.187). Every pool is different animals
+#   (replicate_genotype_check.txt). Compare IOCAS2024_OA_TRANSGEN, which
+#   failed with 0.061 against 0.051.
+# - No pseudo-replication symptoms: 111 of 28,333 genes at padj < 0.05 (not
+#   ~40%), median lfcSE 0.19 for genes with baseMean > 100. Heat shock
+#   protein 68 (LOC117680673) is among the most significant heat-induced genes
+#   (log2FC 4.4).
+# - Warnings: the HSF1-based selection of sequenced animals and the unknown
+#   container structure (see the header).
+qc_status: "passed_with_warnings"
+analysis_status: "harmonized"
+
+# One comparison, prespecified 2026-10-12 before any result: heat shock vs
+# untreated control. The RNAi and RNAi + heat groups test HSF1 regulation (a
+# knockdown, i.e. mechanism) and are not used. stress_response: no tolerance
+# outcome was measured for these animals.
+comparisons:
+  - comparison_id: "heat_35c_2h_vs_control"
+    tissue: "gill"
+    life_stage: "juvenile"
+    stressor_original: "heat shock in seawater at 35 ± 0.7 °C for 2 h (group 2, 'HS'), vs untreated control (group 1) after 1 week at 12 ± 1 °C (Liu et al. 2019)"
+    stressor_standardized: "temperature"
+    exposure_intensity: "35 C seawater vs 12 C acclimation"
+    exposure_duration: "2 h"
+    exposure_timing: "acute heat shock; gill sampling time after heat shock as in the paper's protocol (heat at 46 h, sampling at 48 h for the RNAi experiment)"
+    control_condition: "untreated control, 3 pooled libraries x 5 oysters (control-1..3)"
+    treatment_condition: "35 C heat shock for 2 h, 3 pooled libraries x 5 oysters (HS-1..3)"
+    phenotype: "thermal_tolerance"
+    phenotype_direction: "not_applicable"
+    phenotype_unit: null
+    resilience_classification: "stress_response"
+    sample_size: 6
+    biological_replicates: 3
+    meta_analysis_primary: true
+    results_file: "data/studies/LIU2019_HEAT_HSF1/LIU2019_HEAT_HSF1_heat_35c_2h_vs_control_dge_standardized.tsv"
+
+quality_flags:
+  - raw_data_available
+  - single_timepoint
+
+limitations: >
+  (1) Sequenced oysters were selected by HSF1 qRT-PCR expression, not at
+  random. (2) Container structure is not described; each treatment group may
+  have been one container, so oysters (and pools) may not be independent
+  replicates of the heat treatment. (3) Each library pools five oysters; n =
+  3 libraries per group. (4) 7-month-old oysters are recorded as juvenile.
+  (5) Acute 2 h shock at 35 C; no tolerance outcome measured.
+
+provenance:
+  registered_by: "sr320"
+  date_registered: "2026-10-12"
+  curation_notes: >
+    Claimed with `aree start-study --accession PRJNA516762 --study-id
+    LIU2019_HEAT_HSF1` (draft PR sr320/AREE#37). Sample sheet from live ENA
+    metadata with `aree fetch-samplesheet --label-field sample_alias` (pattern
+    in config/LIU2019_HEAT_HSF1.config): 12 runs, 3 per group. The six control
+    and HS FASTQs were already on the omics drive from an earlier sr320/AREE-co
+    pass; all 12 files matched ENA's MD5s on 2026-10-12 before use. Replication
+    and the HSF1-based selection of sequenced animals read from the paper's
+    methods (PMC6688261). An earlier reanalysis in sr320/AREE-co reported 99 of
+    22,397 genes at FDR < 0.05 for this contrast.
+    Run 2026-10-12 (Nextflow 26.04.7, native -profile local,workstation, 24/24
+    tasks): Salmon mapping 77.7-79.8%, library type IU. Harmonized: 28,333
+    evidence records.
+  source_links:
+    - "https://doi.org/10.1186/s12864-019-6003-8"
+    - "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688261/"
+    - "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA516762"