Repository navigation
Conversation
…, gill C. gigas gill at 0, 6 and 48 h after Vibrio alginolyticus infection, n=3 (Ocean University of China, 2020). It joins the Vibrio pool. It is likely paired with WGBS deposit PRJNA1113357: both deposits label libraries with the same codes (0hg1 ... 48hg3 gill), which would make this AREE's first real RNA-seq + methylation pair on one contrast. Publication inferred: Li JA et al. 2024, Fish Shellfish Immunol 151:109705 (WGBS at 0/6/48 h, integrated with the transcriptome; Liu S, Li Q). Two prespecified comparisons vs 0 h; 48 h is meta_analysis_primary. Both are disease on disease_susceptibility, following CALLA and HESSER. Pre-screen passed (0h 0.167, 6h 0.046, 48h 0.017). The 0 h baseline is unusually variable and is flagged for a PCA check in the full run. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This branch has not been deployed
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Claimed by
aree start-studyon Pori, 2026-10-15. Draft until the run is finished.Study
LI2024_VIBRIO_GILLPRJNA830931(SRR19046233–41); DOI 10.1016/j.fsi.2024.109705 (inferred); paired WGBSPRJNA1113357Checklist
aree validate-study registry/studies/<STUDY_ID>.yamlpassesaree fetch-samplesheet, not hand-writtendata/studies/<STUDY_ID>/, with parameters, tool versions and input checksumswork/orresults/qc_statusandanalysis_statusin the YAML reflect what was actually runtests/test_<study>_study.pypin the decisions that are easy to erode laterCuration decisions
Design. C. gigas gill at 0, 6 and 48 h after V. alginolyticus infection, n=3, one BioSample per oyster (Ocean University of China, Laizhou, 2020-10).
Paired methylome. The WGBS deposit
PRJNA1113357uses the same library codes (0hg1…48hg3gill). That makes it likely the same nine oysters have both RNA-seq and methylation data, which would be AREE's first real RNA-seq + methylation pair on one contrast. The WGBS isn't registered here.Comparisons: 48 h vs 0 h (primary) and 6 h vs 0 h, both
diseaseondisease_susceptibility. The only control is the 0 h baseline, so infection is confounded with time.Paper (inferred): Li JA et al. 2024, Fish Shellfish Immunol 151:109705.
Pre-screen passed: 0h 0.167, 6h 0.046, 48h 0.017. The 0 h baseline is unusually variable, so check a PCA in the full run. Exclude an animal only on independent evidence.
🤖 Generated with Claude Code