Evidence card: NCBI:GeneID:105332871

Real public-study evidence. Association evidence only; not a validated biomarker.

How to interpret expression as evidence for resilience. Differential expression alone does not establish a resilience marker; higher expression does not necessarily mean greater resilience.

This feature was selected among up to ten displayed findings in at least one study. All available rows for it are shown below, including nonsignificant and exploratory results. Presence in multiple datasets does not establish independent replication: exposures, tissues, life stages, and phenotype meanings differ. No cross-study score or pooled effect is calculated.

Guide to effect sizes, uncertainty and gene descriptions.

Study-specific effects

Study / design	RefSeq description	Contrast	Effect scale	Effect	Standard error	Adjusted p-value	Interpretation
CGIG_HEAT24H_RNASEQ_PRJNA407831	uncharacterized LOC105332871	35C_24h_vs_0h_gill	log2 fold change	0.5246	0.8288	not available	Study-level association; see design caveats
CGIG_HEAT6H_RNASEQ_PRJNA407831	uncharacterized LOC105332871	35C_6h_vs_0h_gill	log2 fold change	0.2743	1.061	0.9469	Study-level association; see design caveats
PRJNA516762	uncharacterized LOC105332871	heat_35C_2h_vs_control_12C	log2 fold change	0.8634	1.44	1	Study-level association; see design caveats
PRJNA735889	uncharacterized LOC105332871	ph_6.5_6.8_vs_ph_7.4_7.8_23d_juveniles	log2 fold change	-2.171	0.7241	0.02236 (nominal only)	Exploratory; tank clustering unmodeled
PRJNA826964	uncharacterized LOC105332871	ocean_acidification_vs_ambient_control	log2 fold change	1.034	1.248	0.8526	Study-level association; see design caveats
PRJNA1329250	uncharacterized LOC105332871	oshv1_microvariant_challenge_vs_unchallenged_control	log2 fold change	4.665	0.9773	5.157e-05	Study-level association; see design caveats
PRJNA593309	uncharacterized LOC105332871	oshv1_cohabitation_48h_vs_0h_21C	log2 fold change	13.99	1.39	1.279e-20	Study-level association; see design caveats
PRJNA756710	uncharacterized LOC105332871	low_salinity_10ppt_vs_30ppt_during_vibrio_infection	log2 fold change	0.8273	1.383	0.7561	Study-level association; see design caveats
CGIG_VIBRIO12H_RNASEQ_PRJNA852380	uncharacterized LOC105332871	vibrio_12h_vs_control_digestive_gland	log2 fold change	-0.2377	0.894	not available	Study-level association; see design caveats
CGIG_VIBRIO24H_RNASEQ_PRJNA852380	uncharacterized LOC105332871	vibrio_24h_vs_control_digestive_gland	log2 fold change	-2.025	0.7217	not available	Study-level association; see design caveats

CGIG_HEAT24H_RNASEQ_PRJNA407831

Phenotype interpretation: Intertidal-origin F1 oysters showed higher survival after acute heat stress (42 C, 1 h) and higher metabolic rates at 35 C than subtidal-origin oysters, with slower growth, and more transcriptional plasticity. AREE records the gill transcriptional response to 35 C averaged over the four populations, not survival per library.

Biological replication: 23 libraries analysed (24 sequenced; one 0 h outlier left out): 11 at 0 h and 12 at 24 h. Each library pools equal gill RNA from five oysters of one culture tank; four populations (two sites x intertidal or subtidal origin) x three tanks, and the same tanks are sampled at each time.

Evidence classification: stress_response. Tissue: gill; life stage: adult.

Quality flags: raw_reanalysis;acute_heat_response;pooled_libraries;population_blocked_contrast;shared_control_group;dependence_group=PRJNA407831_0h_pools;heat_24h;deseq2_significance_unavailable.

Study limitations:

Both AREE records from this study (the other is CGIG_HEAT6H_RNASEQ_PRJNA407831, 6 h) test against the same twelve 0 h pools, so they carry the dependence group PRJNA407831_0h_pools and count as one replication group.
Each library pools gill RNA of five oysters, so the error model describes tank-pool variation, not variation between animals. The sister IOCAS study PRJNA826964 deposited resequenced RNA as replicates, so these pools were checked with the expressed-SNP test (scripts/check_replicate_genotypes.py) before analysis.
The model blocks on the four source populations (~ population + condition), so the effect is averaged over intertidal and subtidal origins and the two sites; the publication’s main result, that intertidal oysters respond with more plasticity, is not part of this record. A tank-paired model (~ tank + condition) is kept as a sensitivity analysis.
Sample aliases code tidal origin as J or X (for example BYQJ01, LTX243); the publication uses I (intertidal) and S (subtidal), and the BioSamples do not record it. J and X are read as the Chinese jian (intertidal) and xia (subtidal), but no AREE result depends on that reading because population is a blocking factor.
One 0 h library, h0_LTJ_2, is left out by AREE’s QC rule (median VST correlation below the median minus three robust SDs); it is the library the publication also discarded (LT-I_0h_2). The exclusion lives in scripts/prepare_prjna407831_fastqs.py.
ENA served other studies at 0.05-0.35 MB/s in October 2026, so all runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the manifest on conversion.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: ba65a504fd1c43fe5df5636afd198fc3f2b95abd6a145604c6ed9ca3caf03421.

CGIG_HEAT6H_RNASEQ_PRJNA407831

Biological replication: 23 libraries analysed (24 sequenced; one 0 h outlier left out): 11 at 0 h and 12 at 6 h. Each library pools equal gill RNA from five oysters of one culture tank; four populations (two sites x intertidal or subtidal origin) x three tanks, and the same tanks are sampled at each time.

Evidence classification: stress_response. Tissue: gill; life stage: adult.

Quality flags: raw_reanalysis;acute_heat_response;pooled_libraries;population_blocked_contrast;shared_control_group;dependence_group=PRJNA407831_0h_pools;heat_6h.

Study limitations:

Both AREE records from this study (the other is CGIG_HEAT24H_RNASEQ_PRJNA407831, 24 h) test against the same twelve 0 h pools, so they carry the dependence group PRJNA407831_0h_pools and count as one replication group.
Each library pools gill RNA of five oysters, so the error model describes tank-pool variation, not variation between animals. The sister IOCAS study PRJNA826964 deposited resequenced RNA as replicates, so these pools were checked with the expressed-SNP test (scripts/check_replicate_genotypes.py) before analysis.
The model blocks on the four source populations (~ population + condition), so the effect is averaged over intertidal and subtidal origins and the two sites; the publication’s main result, that intertidal oysters respond with more plasticity, is not part of this record. A tank-paired model (~ tank + condition) is kept as a sensitivity analysis.
Sample aliases code tidal origin as J or X (for example BYQJ01, LTX243); the publication uses I (intertidal) and S (subtidal), and the BioSamples do not record it. J and X are read as the Chinese jian (intertidal) and xia (subtidal), but no AREE result depends on that reading because population is a blocking factor.
One 0 h library, h0_LTJ_2, is left out by AREE’s QC rule (median VST correlation below the median minus three robust SDs); it is the library the publication also discarded (LT-I_0h_2). The exclusion lives in scripts/prepare_prjna407831_fastqs.py.
ENA served other studies at 0.05-0.35 MB/s in October 2026, so all runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the manifest on conversion.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 3ff5b26926b5dc5ac2b94196d5b5a8628742dc7a4ebf2460da80389567311c2a.

CGIG_HEAT_RNASEQ_PRJNA516762

Phenotype interpretation: Organism-level thermal-tolerance direction was not measured; molecular heat-response direction only

Biological replication: Direct heat-versus-control contrast: 3 pooled RNA-seq libraries per condition, each pooling 5 individuals (30 individuals total; 6 libraries)

Evidence classification: stress_response. Tissue: gill; life stage: juvenile.

Quality flags: raw_reanalysis;acute_heat_response;pooled_libraries.

Study limitations:

This intake represents molecular heat-stress response, not a direct survival or organism-level thermal-tolerance measurement.
Each RNA-seq library pooled gill RNA from five oysters, so individual-level variability is unavailable.
AREE independently reanalyzed the raw reads against GCF_963853765.1/RS_2024_06; the original study used legacy assembly GCA_000297895.1 and CGI/newGene identifiers, so these results are a current-reference reanalysis rather than an exact reconstruction of the publication pipeline.
The direct heat-versus-control contrast yields modest differential expression (99 genes at FDR <= 0.05 of 22,397 tested), and PC1 (26.3% of variance) separates most but not all libraries, with heat_A overlapping the controls.
The HSF1 RNAi-only and RNAi-plus-heat contrasts are preserved in the source workbook but excluded from this direct heat-versus-control reanalysis.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: f0bded9f7662170c4985ff78b455a69e7df0b43c114895da85277159a2daba88.

CGIG_OA_RNASEQ_PRJNA735889

Phenotype interpretation: Lutier et al. report physiological tipping points at pHT 7.3-6.9 that coincide with a major reshuffling of the transcriptome and membrane lipids; AREE records the whole-animal transcriptional response below the tipping window relative to above it, not a measured tolerance phenotype

Biological replication: 50 oysters, one whole-animal library each: 25 control and 25 acidified, 5 per tank. A 51st library, 13Ebis, is a resequencing of oyster 13E and is not analysed. Each pH level is one tank, so oysters are replicates within tank and the 10 tanks are the replicates of the pH contrast.

Evidence classification: environmental_exposure. Tissue: whole_organism; life stage: juvenile.

Quality flags: raw_reanalysis;ocean_acidification_response;ph_band_contrast_tipping_window_excluded;no_ambient_ph_reference;one_tank_per_ph_level;gametogenesis_blocked_contrast;fdr_lt_0.05;exploratory_tank_clustering_unmodeled.

Exploratory uncertainty: Tank clustering is unmodeled. Standard errors and adjusted p-values above are nominal only; this row is excluded from pooling and significance rewards.

Study limitations:

The study is a 15-level pH gradient (pHT 6.5-7.8, 76 libraries). AREE reduces it to a two-group contrast at the authors’ tipping-point window: the five tanks inside pHT 7.3-6.9 (tanks 1, 6, 4, 11 and 10; 25 libraries) are excluded and not downloaded. Effect sizes are therefore log2 fold changes between two pH bands, not slopes per pH unit, and they mix the response across five pH levels on each side.
There is no ambient-pH tank; the reference band (pHT 7.4-7.8) is itself below present-day coastal pH, so the contrast understates the full response to acidification.
Each pH level is a single tank, so tank and pH are confounded at the level of a single pH; with five tanks per band the band contrast has tank-level replication, but DESeq2 treats the 50 analysed oysters as independent and does not model tank. Standard errors, p-values and FDR values are exploratory and may overstate precision. A tank-aware reanalysis is required before inferential use; PCA and per-tank residual checks do not correct the error model.
Tank 15 is labelled ‘pHT 6.5 bis’ in BioSample: a second tank at pHT 6.5 alongside tank 9.
Library 13Ebis (SRR14803132) has a different index from 13E (SRR14803133) and about half its reads. The expressed-SNP check shows it is the same oyster (allele-frequency difference 0.026, below the 0.032 expected for one RNA resequenced; the next closest pair differs by 0.198), so it is kept in the manifest but left out of the analysis.
Male gametogenesis is unbalanced between bands: a spermatogenesis module is active in 11 of 25 control and 2 of 25 acidified oysters (Fisher p = 0.008), spread across all five control tanks, which suggests that low pH delays or suppresses the onset of spermatogenesis in 5-month-old juveniles. The primary model blocks on this call (~ gametogenesis + condition) so the evidence records a gametogenesis-adjusted association with pH, without establishing a direct causal response; the unadjusted model is kept as a sensitivity analysis. The call is a transcriptional proxy derived from the same data (scripts/score_prjna735889_gametogenesis.py), not a histological sex or maturation call, and with only two active acidified oysters the gametogenesis effect is estimated mostly from the control band.
Condition, tank and pH come from the NCBI BioSample title, treatment and growth_protocol attributes; every library is paired-end. ENA served the FASTQs at about 80 KB/s on 2026-10-02, so all 51 runs are taken from the NCBI Open Data mirror as .sra archives checked against the size and MD5 NCBI publishes (CGIG_OA_RNASEQ_PRJNA735889_sra_locations.tsv), and each converted FASTQ pair must match the manifest read count.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: a8f7485ec9436cc334d22b6819d7137f37dccb753fa688700c49d264cb7c0dda.

CGIG_OA_RNASEQ_PRJNA826964

Phenotype interpretation: The BioProject title frames acidification as compromising energy management; AREE records the hepatopancreas transcriptional response to acidification, not a measured organism-level energetic or survival phenotype

Biological replication: 6 pooled RNA samples, one per arm at each of 7, 28 and 56 days, each sequenced as three libraries (18 libraries); the BioSample records call the libraries biological replicates, but their genotypes show each set of three is one pool of several oysters

Evidence classification: stress_response. Tissue: hepatopancreas; life stage: not_recorded.

Quality flags: raw_reanalysis;ocean_acidification_response;timepoint_blocked_contrast;pooled_rna_samples;possible_genetic_background_confound.

Study limitations:

No publication is linked to the BioProject, and searches of PubMed, Europe PMC full text and Crossref on 2026-09-28 found none, so there are no published methods, results or effect tables to reconcile the reanalysis against.
The acidification intensity (target pH or pCO2), seawater carbonate chemistry, temperature and oyster size or age are not recorded in the public metadata, so exposure intensity and life stage are unresolved.
The treatment was probably CO2-driven acidification to pH 7.50. This is inferred, not documented: the same IOCAS group (L. Qiu and colleagues) ran C. gigas CO2 exposures at pH 7.50 sampled from 7 to 56 days (Wang et al. 2021, Ecotoxicol Environ Saf, doi:10.1016/j.ecoenv.2021.112235) and at pH 7.50 for 7 and 60 days (Wang et al. 2020, Sci Total Environ, doi:10.1016/j.scitotenv.2020.140177), and reported hepatopancreas responses to acidification over about two months (Zhang et al. 2021, J Oceanol Limnol, doi:10.1007/s00343-021-0462-x). None of these papers is linked to PRJNA826964, and the closed-access hepatopancreas paper, the most likely companion, has not been checked against it.
The primary AREE contrast compares the three acidified pools with the three control pools and blocks on sampling day (~ timepoint + condition); it estimates an acidification effect averaged over 7, 28 and 56 days rather than time-specific or acclimation effects, and it has only two residual degrees of freedom.
The three libraries per day-by-condition cell are technical replicates of one pooled RNA sample, not the independent biological replicates the BioSample attributes state. Expressed-SNP allele frequencies (scripts/check_replicate_genotypes.py, 4M read pairs per library) agree within a cell to within resequencing noise and show no single-animal genotype peaks, and within-cell expression dispersion is 2.7% BCV against 10.8-22.4% in the other AREE oyster studies. Treating the 18 libraries as replicates inflates significance roughly twelvefold, so the libraries are summed into 6 pools (–collapse-by=condition+timepoint).
Each pool is a different set of animals, and the acidified pools are genetically further from the controls (mean allele-frequency difference 0.24-0.31) than the control pools are from one another (0.085-0.19), so acidified and control oysters may come from different stocks or families. Several of the strongest effects are 4-6 log2 changes in transposon-derived genes (tigger, HARBI1), the pattern expected from presence-absence variation between genetic backgrounds, so part of the contrast may be genetic rather than an acidification response. The evidence is harmonized with every row flagged pooled_rna_samples and possible_genetic_background_confound, so scoring discounts it and evidence cards list the caveat; treat it as provisional acidification evidence until a design with shared genetic backgrounds confirms it.
Condition, sampling day and replicate were taken from NCBI BioSample treatment and replicate attributes and agree with the library names (C/O = control/acidified, followed by day and replicate).
The BioProject carries no author-deposited processed expression matrix.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 4a01845d837665c4e977190e7e9111a2d5a7bd3e5f38d89ca473276a96b26f2c.

CGIG_OSHV1_RNASEQ_PRJNA1329250

Phenotype interpretation: Infection up-regulated antiviral defense transcripts, including RIG-I-like receptors and the interferon-like pathway, similarly in both lineages; AREE records molecular antiviral responsiveness, not an organism-level survival difference

Biological replication: 42 RNA-seq libraries: 12 controls (6 Midori, 6 Miyagi) and 30 OsHV-1 microvariant-challenged (15 Midori, 15 Miyagi, split across USA, Australia, and France viral strains at 5 libraries per lineage-strain cell)

Evidence classification: disease_associated. Tissue: whole_soft_tissue; life stage: spat.

Quality flags: raw_reanalysis;pathogen_challenge_response;lineage_balanced_contrast;fdr_lt_0.05.

Study limitations:

This intake represents the molecular antiviral response to experimental OsHV-1 microvariant challenge, not a measured survival or organism-level disease-resistance difference between the two lineages.
Challenge dose, exposure duration, and time of sampling after inoculation are not recorded in the public SRA metadata, so exposure intensity and duration are unresolved.
The challenged and control arms are unequal in size (30 versus 12 libraries), but lineage is balanced within each arm and within every viral strain: 6 Midori and 6 Miyagi controls, and 5 of each lineage for each of the Australia, France, and USA strains. The lineage effect is therefore not confounded with infection status, and AREE blocks on lineage as ~ population + condition.
The publication contrasts the USA and Australia microvariant strains and reports no marked difference between them; the France-strain libraries are present in the BioProject and are pooled into the challenged arm of the AREE contrast rather than analyzed as a separate strain effect.
The BioProject carries no author-deposited processed expression matrix, so AREE has no published feature-level effect table to reconcile against.
Condition, lineage, and viral-strain assignments were reconstructed from NCBI BioSample attribute tags rather than from a supplementary sample table; the source metadata spells the Miyagi lineage ‘Myagi’, which AREE normalized.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 3beb15844b8040ff58c64acd452381f853bbbacb730cce2bf434b6ee05d41f2e.

CGIG_OSHV1_RNASEQ_PRJNA593309

Phenotype interpretation: At 21 C survival 14 days after cohabitation was 52.4%, and OsHV-1 DNA had reached high levels in all three oysters sampled at 48 h. AREE records the whole-oyster transcriptional response to infection, not survival per library.

Biological replication: 6 libraries, one whole 8-month-old oyster per tank: three at 0 h and three at 48 h, the same three 21 C tanks sampled at both times.

Evidence classification: disease_associated. Tissue: whole_organism; life stage: juvenile.

Quality flags: raw_reanalysis;pathogen_challenge_response;unpaired_primary_tank_paired_sensitivity;one_oyster_per_tank;dependence_group=PRJNA593309_21C_tanks;fdr_lt_0.05.

Study limitations:

The 0 h and 48 h oysters come from the same three tanks. The primary model is unpaired (~ condition); a tank-paired model (~ tank + condition) is kept as a sensitivity analysis.
One whole oyster per tank was sequenced at each time point, with three replicate tanks per temperature (45 l tanks), so libraries are tank-level replicates and the contrast has three tanks per arm.
The two AREE records from this study use different oysters but the same three 21 C tanks (the 21 C 12 h oysters of CGIG_HEAT_RNASEQ_PRJNA593309 and the 21 C 0 h and 48 h oysters of CGIG_OSHV1_RNASEQ_PRJNA593309), so both carry the dependence group PRJNA593309_21C_tanks and count as one replication group.
The BioSamples give a collection date of 2019-05-19, but the publication dates the experiment to May 2016; the experimental groups follow the sample aliases (Cg_<CTR | OsHV>hpc_), which agree with the publication’s design.
The study also deposited libraries at 26 C and at 24 and 96 h; the publication does not analyse the 26 C libraries, and AREE uses only the time points of its two contrasts.
The publication aligned reads with STAR to the Ensembl oyster genome v9.38 and tested with edgeR; AREE quantifies against GCF_963853765.1/RS_2024_06 with Salmon and DESeq2.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: cca3b26b0a11f8cd29467b1df45d728788247bf18855e27becda42e3e88e27d8.

CGIG_SALINITY_RNASEQ_PRJNA756710

Phenotype interpretation: Higher mortality after Vibrio infection is unfavorable; infected oysters reached 100% mortality at 10 ppt versus 33% at 30 ppt over 12 days (log-rank p < 0.01, n = 30 per tank in triplicate). AREE records the gill transcriptional response to low salinity during infection, not survival per library.

Biological replication: 12 RNA-seq libraries used for the contrast: 6 at 30 ppt and 6 at 10 ppt, three per salinity at each of 12 h and 48 h. Each library pools equal gill tissue from three oysters taken from one tank. Two further 0 h libraries (SRR15559848, SRR15559847) are shared pre-transfer baselines with no salinity contrast and are not used.

Evidence classification: disease_associated. Tissue: gill; life stage: not_recorded.

Quality flags: raw_reanalysis;low_salinity_response;infection_background_all_arms;timepoint_blocked_contrast.

Study limitations:

Every sequenced oyster was infected with Vibrio alginolyticus, so the contrast estimates the effect of low salinity during infection, not of low salinity alone. The uninfected, sham-injected controls held at 30 ppt were used for the survival curve only and were not sequenced. stressor_class is salinity because salinity is the only factor that differs between the contrasted arms.
The primary AREE contrast pools 12 h and 48 h and blocks on sampling time (~ timepoint + condition). It estimates a low-salinity effect averaged over the two times, whereas the publication tested each time separately; each time-by-salinity cell has only three libraries.
Each salinity arm used three tanks, and a pool of three oysters was taken from each tank at each time, so the 12 h and 48 h libraries with the same replicate number may share a tank. The public metadata do not state that replicate numbers correspond to tanks, so the model does not pair them.
Oyster age or size class is not given beyond an average wet weight of 18.2 +/- 2.8 g, so life_stage is not recorded. Temperature during the challenge is not reported.
The library names use C23 for the normal-salinity arm, but the publication and BioSample titles give the normal salinity as 30 ppt; C10 matches the 10 ppt arm.
Condition, time and replicate come from the NCBI BioSample titles. They agree with the library names (C10/C23 followed by 1-3 for 12 h and 4-6 for 48 h), and the raw read count of every library matches publication Supplementary Table 3.
The publication aligned reads with HISAT2 to GCA_902806645.1, counted them with featureCounts and ran DESeq2 per time point (padj < 0.05, |fold change| > 1). It reports 3,038 DEGs at 12 h (1,731 higher, 1,307 lower at 10 ppt) and 3,187 at 48 h (1,656 higher, 1,531 lower) in Supplementary Table 4, keyed by RefSeq LOC identifiers. Only significant genes are listed, so the table cannot be used as a full ranked result.
The companion 16S rRNA amplicon data for the digestive gland are in the separate BioProject PRJNA756403 and are outside this record.
Against the publication’s per-time DEGs (Supplementary Table 4), 5,206 of 6,225 LOC identifiers map directly to a current GeneID. Of those tested here, 96.0% (12 h) and 95.7% (48 h) change in the same direction in the pooled AREE model, fold changes correlate at r = 0.784 and 0.759, and none is significant in the opposite direction; 44% reach FDR < 0.05 in the pooled model.
rRNA genes are over-represented among low-salinity-higher genes (10 observed versus 0.8 expected; adjusted p = 1.2e-10), which points to a difference in residual rRNA between arms rather than a biological response; those loci should not be interpreted.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 39f1098bfe2737737332f9e0cd5fdcd64159c848ac8f8562e1d8912615e59fe9.

CGIG_VIBRIO12H_RNASEQ_PRJNA852380

Phenotype interpretation: No phenotype is deposited; AREE records the digestive-gland transcriptional response to Vibrio exposure.

Biological replication: 6 digestive-gland libraries: 3 controls and 3 at 12 h after Vibrio exposure. Each library is a pool by expressed-SNP genotype; pool size is not recorded.

Evidence classification: disease_associated. Tissue: digestive_gland; life stage: juvenile.

Quality flags: raw_reanalysis;pathogen_challenge_response;pooled_libraries;vibrio_species_not_stated;no_linked_publication;shared_control_group;dependence_group=PRJNA852380_controls;vibrio_12h;deseq2_significance_unavailable.

Study limitations:

No publication is linked. The Vibrio species, dose and exposure route are not recorded; the submitting group’s 2022 study (Liu et al., Fish Shellfish Immunol 131:1027-1039) used Vibrio mediterranei, and a 2025 study describes digestive-gland data after V. parahaemolyticus at 12 and 24 h, but neither is confirmed to be this dataset.
The two AREE records from this study (12 h and 24 h) test against the same three control libraries, so they carry the dependence group PRJNA852380_controls and count as one replication group.
Groups come from the SRA sample names (control1-3, Vh_), which agree with the BioSample replicate attributes.
All runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the NCBI spot counts on conversion.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 3484a36bd3fc9e7ca5eb367ded0e5847e78e02de5f9a07d6243b43502e0a2db2.

CGIG_VIBRIO24H_RNASEQ_PRJNA852380

Phenotype interpretation: No phenotype is deposited; AREE records the digestive-gland transcriptional response to Vibrio exposure.

Biological replication: 6 digestive-gland libraries: 3 controls and 3 at 24 h after Vibrio exposure. Each library is a pool by expressed-SNP genotype; pool size is not recorded.

Evidence classification: disease_associated. Tissue: digestive_gland; life stage: juvenile.

Study limitations:

No publication is linked. The Vibrio species, dose and exposure route are not recorded; the submitting group’s 2022 study (Liu et al., Fish Shellfish Immunol 131:1027-1039) used Vibrio mediterranei, and a 2025 study describes digestive-gland data after V. parahaemolyticus at 12 and 24 h, but neither is confirmed to be this dataset.
The two AREE records from this study (12 h and 24 h) test against the same three control libraries, so they carry the dependence group PRJNA852380_controls and count as one replication group.
Groups come from the SRA sample names (control1-3, Vh_), which agree with the BioSample replicate attributes.
All runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the NCBI spot counts on conversion.

Provenance: Reference GCF_963853765.1 / RS_2024_06; mapping exact; workflow 0.1.0.

Harmonized evidence. Processed input. Input SHA-256: 5571ce917cf19997c36f6355b662989aae8ab9a46b93cdcba8c42dd77b580264.

Next validation step

Independent biological replication with matched exposure and measured phenotype, an appropriate experimental-unit model, and targeted validation in the relevant tissue and life stage.