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candidate_studies: record three rejections and two outcomes - #50
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- PRJNA341808 (larval bacteria/heat, IOCAS): rejected after an expressed-SNP screen on ~2 M reads per run showed each arm is one RNA pool. - PRJNA694496 (thermotolerance-selected line): rejected, groups cannot be recovered from the deposit or the paper. - PRJNA877226 (Tier 2 #9): rejected, infected-only 12 h vs 48 h, no control. - PRJNA1196326 (Tier 2 #8): failed QC as IOCAS2024_OA_TRANSGEN (#17). - PRJNA913164 (Tier 2 #6): registered as GEORGE2023_HEATWAVE_PLOIDY (#18); it is published (George et al. 2023). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
main rejected PRJNA341808 independently (2026-10-14) with scripts/prescreen_replicates.py. Resolved by keeping main's account and table row (plus the rejection marker), and adding the expressed-SNP result as agreeing but not decisive on its own: large larval pools from one cross converge on their parents' allele frequencies, as main's text notes. The "lessons" paragraph now points at the pre-screen script and states the genotype check's limit. The other three entries (IOCAS2024, PRJNA694496, PRJNA877226) are kept. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Docs only: updates
docs/candidate_studies.mdwith recent screen-outs so nobody curates them again.Rejected:
PRJNA694496(thermotolerance-selected line): the groups can't be recovered. There's one BioSample for all runs, vendor run IDs, and no mapping in the paper.PRJNA877226(Tier 2 [study] CIBNOR2021_HEAT_RRSS (PRJNA690951) #9): infected-only, 12 h vs 48 h, with no control. It is likely the high-temperature arm of [study] LI2022_LOWSAL_VIBRIO (PRJNA756710) #26's experiment; borrowing [study] LI2022_LOWSAL_VIBRIO (PRJNA756710) #26's controls across BioProjects is not done.PRJNA341808(larval bacteria / heat):mainrejected it independently on 2026-10-14 withscripts/prescreen_replicates.py, and that account is kept as the primary one. This PR adds my expressed-SNP result (within-group 0.062 vs 0.057 one-RNA noise) as agreeing but not decisive: large larval pools from one cross converge on their parents' allele frequencies either way, asmain's text notes.Outcomes:
PRJNA1196326(Parse per-run design labels for single-BioSample deposits #8): failed QC asIOCAS2024_OA_TRANSGEN([study] IOCAS2024_OA_TRANSGEN (PRJNA1196326) #17).PRJNA913164(Obtain the heat-resistant / heat-susceptible family RNA-seq data (Arredondo-Espinoza et al. 2023) #6): registered asGEORGE2023_HEATWAVE_PLOIDY([study] GEORGE2023_HEATWAVE_PLOIDY (PRJNA913164) #18). It is published (George et al. 2023).Lessons paragraph: one BioSample per group is the cheapest early warning of pseudo-replication. Replication can be checked before download with
prescreen_replicates.py. The genotype check complements it for single animals or small pools, but not for large sibling pools.Merge conflict with
mainresolved (2026-10-15): both sides had edited thePRJNA341808table row and the Rejected section.🤖 Generated with Claude Code