| CGIG_HEAT_RNASEQ_001 |
nan |
Simulated C. gigas heat challenge RNA-seq study for AREE MVP. |
Crassostrea gigas |
rnaseq |
gill |
juvenile |
temperature |
thermal_tolerance |
resilience_associated |
24 |
simulated_public_demo |
demo_harmonized |
simulated_pass |
| CGIG_HEAT_RNASEQ_002 |
nan |
Simulated C. gigas family heat survival RNA-seq study for AREE MVP. |
Crassostrea gigas |
rnaseq |
mantle |
adult |
temperature |
survival |
resilience_associated |
20 |
simulated_public_demo |
demo_harmonized |
simulated_pass |
| CGIG_OA_METHYL_001 |
nan |
Simulated C. gigas ocean acidification methylation study for AREE MVP. |
Crassostrea gigas |
methylation |
mantle |
juvenile |
ocean_acidification_pH |
acidification_tolerance |
resilience_associated |
18 |
simulated_public_demo |
demo_harmonized |
simulated_pass |
| CGIG_PATH_PROTEO_001 |
nan |
Simulated C. gigas pathogen challenge proteomics study for AREE MVP. |
Crassostrea gigas |
proteomics |
hemolymph |
adult |
pathogen_challenge |
disease_resistance |
disease_associated |
16 |
simulated_processed_only |
demo_harmonized |
processed_qc_available |
| CGIG_SALINITY_METAB_001 |
nan |
Simulated C. gigas salinity stress metabolomics study for AREE MVP. |
Crassostrea gigas |
metabolomics |
whole_body |
juvenile |
salinity |
salinity_tolerance |
resilience_associated |
14 |
simulated_processed_only |
demo_harmonized |
simulated_pass_with_annotation_uncertainty |
| CGIG_LARVAL_PROCESSED_001 |
nan |
Simulated C. gigas larval performance processed-results-only study for AREE MVP. |
Crassostrea gigas |
processed_results_only |
larvae |
larva |
multi_stressor_exposure |
larval_viability |
suggestive |
12 |
simulated_processed_only |
demo_harmonized |
limited_metadata |
| CGIG_HEAT_RNASEQ_PRJNA516762 |
10.1186/s12864-019-6003-8 |
Liu Y, Li L, Huang B, Wang W, Zhang G. RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress. BMC Genomics. 2019;20:639. |
Crassostrea gigas |
rnaseq |
gill |
juvenile |
temperature |
thermal_tolerance |
stress_response |
30 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 154,861,045 read pairs quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; mapping rates 73.85-75.95%; 99 of 22,397 tested genes reach FDR < 0.05 (57 heat-higher, 42 heat-lower); PC1 explains 26.3% of variance and separates most heat from control libraries though heat_A overlaps the controls |
| CGIG_THERMOTOL_RNASEQ_PRJNA694496 |
10.3389/fphys.2021.663023 |
Tan Y, Cong R, Qi H, Wang L, Zhang G, Pan Y, Li L. Transcriptomics Analysis and Re-sequencing Reveal the Mechanism Underlying the Thermotolerance of an Artificial Selection Population of the Pacific Oyster. Front Physiol. 2021;12:663023. |
Crassostrea gigas |
rnaseq |
whole_larva |
umbo_larva |
temperature |
thermal_tolerance |
resilience_associated |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 132,413,989 read pairs quantified with Salmon 1.10.3; mapping rates 42.13-63.94%; PC1 explains 90.6% of variance and separates selected from control; selected_A is displaced on PC2 and has six genes above the Cook’s-distance threshold, but leave-one-out effects correlate 0.962 with the primary model and preserve the direction of all 8,802 primary significant genes |
| CGIG_OSHV1_RNASEQ_PRJNA1329250 |
10.1016/j.fsi.2026.111154 |
Calla B, Thompson NF, Burge CA. Population-specific transcriptomics of Pacific oyster after exposure to a highly pathogenic, globally distributed virus. Fish Shellfish Immunol. 2026;171:111154. |
Crassostrea gigas |
rnaseq |
whole_soft_tissue |
spat |
pathogen_challenge |
immune_responsiveness |
disease_associated |
42 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 1,564,162,034 read pairs quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; mapping rates 44.24-61.66% (median 55.93%), well below the 73.9-76.0% of PRJNA516762 but uniform across arms (control 57.0% versus challenged 55.4%, Welch p = 0.30) and across both lineages, so it reflects library preparation rather than viral reads displacing host reads; 5,446 of 25,734 tested genes reach FDR < 0.05 (3,237 challenge-higher, 2,209 challenge-lower); PC1 explains 59.1% of variance and orders challenged above control though six control libraries fall inside the challenged range, and PC2 (16.6%) tracks the Midori/Miyagi split that ~ population + condition blocks on |
| CGIG_OA_RNASEQ_PRJNA826964 |
nan |
Institute of Oceanology, Chinese Academy of Sciences. The compromised energy management of Pacific oysters (Crassostrea gigas) under ocean acidification conditions. NCBI BioProject PRJNA826964; public 2022. No linked publication identified. |
Crassostrea gigas |
rnaseq |
hepatopancreas |
not_recorded |
ocean_acidification_pH |
metabolic_resilience |
stress_response |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 435,657,730 read pairs quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; mapping rates 78.62-81.26% (median 79.79%), equal across arms (control 79.9% versus acidified 79.9%); expressed-SNP allele frequencies at 2,837 sites show the three libraries in each day-by-condition cell are one pooled RNA sample (within-cell mean difference 0.040-0.057 against 0.039 expected from resequencing the same RNA, r = 0.95; between cells 0.078-0.317), so the 18 libraries were collapsed to 6 pools and tested as ~ timepoint + condition; 890 of 24,681 tested genes reach FDR < 0.05 (301 acidified-higher, 589 acidified-lower) against 10,797 when the libraries were treated as replicates; PC1 (35.9%) separates acidified_d56 from the other five pools and PC2 (29.7%) separates the arms |
| CGIG_SALINITY_RNASEQ_PRJNA756710 |
10.3389/fimmu.2022.859975 |
Li X, Yang B, Shi C, Wang H, Yu R, Li Q, Liu S. Synergistic interaction of low salinity stress with Vibrio infection causes mass mortalities in the oyster by inducing host microflora imbalance and immune dysregulation. Front Immunol. 2022;13:859975. |
Crassostrea gigas |
rnaseq |
gill |
not_recorded |
salinity |
disease_susceptibility |
disease_associated |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 260,215,874 read pairs quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; mapping rates 70.78-80.24% (median 76.97%), consistent with the 73.9-82.5% the publication reports against GCA_902806645.1 and flat across arms (30 ppt 77.7% versus 10 ppt 76.6%, Welch p = 0.49); 3,045 of 21,098 tested genes reach FDR < 0.05 (1,825 low-salinity-higher, 1,220 lower); PC1 explains 27.9% of variance and separates all six 10 ppt libraries from all six 30 ppt libraries; low_salinity_h12_2 is displaced on PC2 and has the most genes above the Cook’s-distance threshold (84), but leaving it out gives effects correlated 0.929 with the primary model, preserves the direction of all 3,045 primary significant genes and retains 2,618 of them at FDR < 0.05 |
| CGIG_OA_RNASEQ_PRJNA1196326 |
nan |
Institute of Oceanology, Chinese Academy of Sciences. Transcriptional acclimation following transgenerational exposure of oysters to ocean acidification. NCBI BioProject PRJNA1196326; public 2024. No linked publication identified. |
Crassostrea gigas |
rnaseq |
whole_larva |
eyed_larva |
ocean_acidification_pH |
acidification_tolerance |
environmental_exposure |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_complete_not_harmonized |
All 121,029,855 read pairs quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 (stranded ISR); mapping rates 68.92-78.45% (median 75.99%), not different between arms (control mean 73.6% versus parental_acidified 76.3%); expressed-SNP allele frequencies at 4,106 sites show the three libraries in each arm are one culture, either one RNA sample or large pools of larvae from one culture (within-arm mean difference 0.061 against 0.051 expected from resequencing the same RNA, r = 0.90), and that the two parental groups are genetically distinct (between arms 0.235 against 0.056, comparable to the 0.271 between two unrelated DECICOMP full-sib families), so parental treatment is fully confounded with parentage and there is one culture per arm; collapsing to one sample per arm leaves 1 v 1, which DESeq2 cannot test, so the 3 v 3 contrast was run for descriptive fold changes only: 10,466 of 21,179 tested genes reach a nominal FDR < 0.05 (5,005 higher, 5,461 lower in parental_acidified), inflated by pseudoreplication; PC1 (94.2%) separates the arms |
| CGIG_STARVATION_RNASEQ_PRJEB86618 |
10.1016/j.isci.2025.114333 |
Duperret L, Valdivieso A, Petton B, Morga B, Faury N, de Lorgeril J, Corporeau C, Degremont L, Allienne JF, Henry S, Turtoi A, Pouzadoux J, Romatif O, Courtay G, Monaco CJ, Toulza E, Lagorce A, Pernet F, Vidal-Dupiol J, Mitta G. Food deprivation enhances disease resistance: Underlying mechanisms in oysters confronted with pacific oyster mortality syndrome. iScience. 2026;29(1):114333. |
Crassostrea gigas |
rnaseq |
whole_soft_tissue |
spat |
nutritional_limitation |
disease_resistance |
resilience_associated |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 318,481,607 single-end reads quantified with Salmon 2.3.4 (sequence-bias correction; GC-bias correction is not fitted for single-end reads) against GCF_963853765.1/RS_2024_06; mapping rates 65.35-69.05% (median 67.26%), below the publication’s 82.3% STAR genome alignment as expected for transcriptome-only quantification, and about two points lower in starved than fed pools (66.2% versus 68.2%, Welch p = 0.0003, with decoy-genome rates 9.8% versus 8.0%); 11,930 of 25,253 tested genes reach FDR < 0.05 (5,941 starved-higher, 5,989 starved-lower); PC1 (49.1%) and PC2 (39.8%) separate the four diet-by-family cells; within-cell BCV is 9.8%, below the 17-38% of the other AREE oyster studies, which fits pools of 10 full sibs. The pools are independent: expressed-SNP allele frequencies at 477 sites differ within cells by 0.098 against 0.042 simulated for one RNA resequenced, and no library shows single-animal genotype peaks |
| CGIG_HAB_RNASEQ_PRJEB18614 |
10.1038/s41598-017-03797-4 |
Payton L, Perrigault M, Hoede C, Massabuau JC, Sow M, Huvet A, Boullot F, Fabioux C, Hegaret H, Tran D. Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum. Sci Rep. 2017;7:3480. |
Crassostrea gigas |
rnaseq |
gill |
adult |
harmful_algal_bloom_exposure |
metabolic_resilience |
stress_response |
24 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 819,493,060 read pairs from 26 one-lane libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 (12 runs from ENA FASTQs, 14 from NCBI .sra archives); mapping rates 68.33-77.33% (median 70.57%). Both day 2 ZT 8.5 pools are contaminated with adductor muscle (myosin, paramyosin, tropomyosin, titin: 23-27% of reads in the top 20 genes against about 6%) and dominated PC1 (79.7%), so the primary contrast drops that time-matched pair (12 versus 12, ~ timepoint + condition): 6,980 of 23,588 tested genes reach FDR < 0.05 (3,690 A. minutum-higher, 3,290 lower), PC1 (35.6%) separates every A. minutum pool from every control, and within-group BCV is 13.7%. With all 26 pools 6,872 genes are significant (log2FC r = 0.982). Blocking also on sequencing pool keeps 99.9% of significant genes in the same direction (log2FC r = 0.794) but only 53.8% significant (4,138 genes), because two of the four pools hold almost one diet each. Mapping is slightly higher in A. minutum pools at matched times (71.3% versus 70.2%, paired p = 0.003) |
| CGIG_OA_RNASEQ_PRJNA735889 |
10.1111/gcb.16101 |
Lutier M, Di Poi C, Gazeau F, Appolis A, Le Luyer J, Pernet F. Revisiting tolerance to ocean acidification: Insights from a new framework combining physiological and molecular tipping points of Pacific oyster. Glob Chang Biol. 2022;28(10):3333-3348. |
Crassostrea gigas |
rnaseq |
whole_organism |
juvenile |
ocean_acidification_pH |
acidification_tolerance |
environmental_exposure |
50 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized_exploratory_tank_clustering_unmodeled |
All 1,717,290,624 read pairs from 50 single-oyster libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 (51 runs from NCBI .sra archives; 13Ebis left out as a resequencing of oyster 13E); mapping rates 71.27-83.67% (median 78.58%), not different between bands (control 78.8% versus acidified 78.0%, Welch t = 1.29). Expressed-SNP allele frequencies at 1,073 sites show every library is one diploid animal (35-47% heterozygous sites) and that oysters differ as much within tanks as between them (0.334 versus 0.335), so tanks were stocked from one cohort and pH is not confounded with genetic background; 13E and 13Ebis differ by 0.026 against 0.032 expected for one RNA resequenced. PC1 of the unadjusted model is a male gametogenesis programme (428 genes at r < -0.9 with PC1: axonemal dyneins, calaxin, ropporin, synaptonemal-complex genes, cyclin B3) active in 11 of 25 control and 2 of 25 acidified oysters (Fisher p = 0.008), spread over all five control tanks. The primary model is ~ gametogenesis + condition (25 v 25): 4,725 of 28,811 tested genes reach nominal FDR < 0.05 under an oyster-level model that does not account for tank clustering; this significance is exploratory (2,735 acidified-higher, 1,990 acidified-lower). The unadjusted ~ condition model gives 6,739; 4,058 genes are significant in both and 97.2% of unadjusted significant genes keep their direction (log2FC r = 0.71). Top genes include a monocarboxylate transporter and Kunitz protease inhibitors up and the shell-matrix protein N66, parathyroid-hormone receptors and arginine kinase down. |
| CGIG_HEAT_RNASEQ_PRJEB86646 |
10.1016/j.scitotenv.2025.180026 |
Duperret L, Valdivieso A, Kunselman E, Petton B, Morga B, de Lorgeril J, Pernet F, Degremont L, Faury N, Allienne JF, Pouzadoux J, Romatif O, Courtay G, Monaco CJ, Toulza E, Delisle L, Vidal-Dupiol J, Lagorce A, Mitta G. Deciphering the molecular mechanisms of oyster resistance to Pacific Oyster Mortality Syndrome (POMS) disease induced by high temperatures. Sci Total Environ. 2025;994:180026. |
Crassostrea gigas |
rnaseq |
whole_soft_tissue |
spat |
temperature |
disease_resistance |
resilience_associated |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 321,328,949 single-end reads quantified with Salmon 2.3.4 (sequence-bias correction; GC-bias correction is not fitted for single-end reads) against GCF_963853765.1/RS_2024_06; mapping rates 64.29-69.05%, about three points lower at 30 C than 23 C (65.5% versus 68.2%, with no overlap between arms), a systematic shift like the two points seen under starvation; 9,024 of 25,355 tested genes reach FDR < 0.05 under ~ family + condition (4,542 higher and 4,482 lower at 30 C); PC1 (60.7%) separates every 30 C pool from every 23 C pool and PC2 (31.1%) separates the families. The pools are independent and temperature is not confounded with genotype: expressed-SNP allele frequencies differ by 0.100 between pools of one family at the same temperature, against 0.040 simulated for one RNA resequenced, and by 0.099 between pools of one family at different temperatures (0.353 between families). Small heat shock proteins are among the strongest 30 C-higher genes (all 7 significant heat shock protein genes are higher), and asparagine synthetase and glycogen-branching enzyme fall. Fold changes are uncorrelated with the starvation contrast that shares these controls (r = -0.05 over 24,836 genes). |
| CGIG_HEAT_RNASEQ_PRJNA913164 |
10.1111/gcb.16880 |
George MN, Cattau O, Middleton MA, Lawson D, Vadopalas B, Gavery M, Roberts SB. Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Glob Chang Biol. 2023;29(24):6969-6987. |
Crassostrea gigas |
rnaseq |
gill |
adult |
temperature |
thermal_tolerance |
stress_response |
44 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
Salmon 2.3.4 (–noLengthCorrection, sequence-bias correction) against GCF_963853765.1/RS_2024_06 on all 72 QuantSeq libraries; mapping rates are low for 3’ tag-seq against the annotated transcriptome (18.7-46.4%, median 34.3%, among the 63 analysed libraries) but similar across arms (control 31.7%, 30 C 33.5%). Nine libraries were left out because their median VST correlation with the other libraries fell below the median minus three robust SDs (0.834): N56, X44, X42, T62, R53, N54 and M43, which the authors also excluded, and R62 and N57; the authors’ eighth exclusion, D54, passes and is kept. Tested as ~ ploidy + condition on counts without the tximport length offset (23 control v 21 30 C): 4,394 of 18,085 tested genes reach FDR < 0.05 (2,216 higher, 2,178 lower); PC1 11.7%, PC2 8.3%. A ploidy-by-treatment likelihood-ratio test finds 10 genes with FDR < 0.05; within-ploidy Wald tests give 2,892 diploid and 2,249 triploid significant genes, with log2 fold changes correlated 0.35 across all tested genes. Of the publication’s diploid and triploid 30 C gene lists, 90.1% and 97.0% of genes tested here change in the same direction (98.5% and 99.4% among genes also significant here). The response: ER chaperones and splicing factors rise (78 kDa glucose-regulated protein, calreticulin, protein disulfide-isomerase A6, SR splicing factors; 13 of 19 significant heat shock protein genes higher) while high-mobility-group proteins and nucleolin fall. |
| CGIG_MULTISTRESS_RNASEQ_PRJNA913164 |
10.1111/gcb.16880 |
George MN, Cattau O, Middleton MA, Lawson D, Vadopalas B, Gavery M, Roberts SB. Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Glob Chang Biol. 2023;29(24):6969-6987. |
Crassostrea gigas |
rnaseq |
gill |
adult |
multi_stressor_exposure |
thermal_tolerance |
stress_response |
42 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
Salmon 2.3.4 (–noLengthCorrection, sequence-bias correction) against GCF_963853765.1/RS_2024_06 on all 72 QuantSeq libraries; mapping rates are low for 3’ tag-seq against the annotated transcriptome (18.7-46.4%, median 34.3%, among the 63 analysed libraries) but similar across arms (control 31.7%, 30 C + 44 C emersion 34.4%). Nine libraries were left out because their median VST correlation with the other libraries fell below the median minus three robust SDs (0.834): N56, X44, X42, T62, R53, N54 and M43, which the authors also excluded, and R62 and N57; the authors’ eighth exclusion, D54, passes and is kept. Tested as ~ ploidy + condition on counts without the tximport length offset (23 control v 19 30 C + 44 C emersion): 3,236 of 17,808 tested genes reach FDR < 0.05 (1,655 higher, 1,581 lower); PC1 12.8%, PC2 10.3%. A ploidy-by-treatment likelihood-ratio test finds 26 genes with FDR < 0.05; within-ploidy Wald tests give 1,979 diploid and 1,347 triploid significant genes, with log2 fold changes correlated 0.30 across all tested genes. Of the publication’s diploid and triploid multiple-stressor gene lists, 98.2% and 96.7% of genes tested here change in the same direction (99.7% and 99.5% among genes also significant here). The response: heat shock protein 68 genes rise up to about 360-fold (log2FC up to 8.5; 14 of 20 significant heat shock protein genes higher) with calreticulin and SR splicing factors, while high-mobility-group proteins and nucleolin fall. |
| CGIG_OSHV1_RNASEQ_PRJNA593309 |
10.1242/jeb.226233 |
Delisle L, Pauletto M, Vidal-Dupiol J, Petton B, Bargelloni L, Montagnani C, Pernet F, Corporeau C, Fleury E. High temperature induces transcriptomic changes in Crassostrea gigas that hinder progress of ostreid herpesvirus (OsHV-1) and promote survival. J Exp Biol. 2020;223(Pt 20):jeb226233. |
Crassostrea gigas |
rnaseq |
whole_organism |
juvenile |
pathogen_challenge |
immune_responsiveness |
disease_associated |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 12 downloaded libraries (96,206,490 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; this record’s six map 49.2-56.0% (0 h 51.5-56.0%, 48 h 49.2-54.3%). Expressed-SNP allele frequencies at 801 sites show each of the six libraries is a different diploid oyster (34-44% heterozygous sites; all pairs differ by 0.28 or more against 0.03 for one RNA resequenced). ~ condition (3 v 3): 846 of 14,555 tested genes reach FDR < 0.05 (663 higher, 183 lower at 48 h); the tank-paired model ~ tank + condition gives 1,025. PC1 explains 44.6% of variance. The response is the expected antiviral programme: all 12 significant interferon-pathway genes rise, with interferon regulatory factor 2, an MDA5-like helicase, baculoviral IAP repeat proteins and E3 ubiquitin ligases. The publication reports 1,413 genes at 48 h against 0 h with edgeR on the Ensembl genome. |
| CGIG_HEAT_RNASEQ_PRJNA593309 |
10.1242/jeb.226233 |
Delisle L, Pauletto M, Vidal-Dupiol J, Petton B, Bargelloni L, Montagnani C, Pernet F, Corporeau C, Fleury E. High temperature induces transcriptomic changes in Crassostrea gigas that hinder progress of ostreid herpesvirus (OsHV-1) and promote survival. J Exp Biol. 2020;223(Pt 20):jeb226233. |
Crassostrea gigas |
rnaseq |
whole_organism |
juvenile |
temperature |
disease_resistance |
resilience_associated |
5 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 12 downloaded libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; mapping is lower at 29 C (44.5-47.6%) than at 21 C (53.5-57.8%) at 12 h. Expressed-SNP allele frequencies at 801 sites show oshv_29C_12h_1 and oshv_29C_12h_2 are one oyster (mean difference 0.025 against 0.029 expected for one RNA resequenced; every other pair differs by 0.28 or more), so their libraries were summed and the contrast is 3 oysters at 21 C against 2 at 29 C. ~ condition: 198 of 14,943 tested genes reach FDR < 0.05 (30 higher, 168 lower at 29 C), against 684 when the duplicated oyster is counted twice. PC1 explains 49.3% of variance. Lower at 29 C are cholesterol transport (NPC intracellular cholesterol transporter) and other metabolic genes, in line with the publication’s down-regulation of metabolism at 29 C; its up-regulated E3 ubiquitin ligase and synaptic receptor genes are not significant here. The publication reports 1,189 genes at 12 h with three libraries per temperature. |
| CGIG_TIRELEACHATE_RNASEQ_PRJNA856813 |
10.1016/j.jhazmat.2024.135742 |
Bernardini I, Tallec K, Paul-Pont I, Peruzza L, Dalla Rovere G, Huber M, Di Poi C, Koechlin H, Quere C, Quillien V, Le Grand J, Le Goic N, Lambert C, Lagarde F, Detree C, Trevisan R, Corporeau C, Patarnello T, Milan M, Huvet A. Effects of tire particles and associated-chemicals on the Pacific oyster (Magallana gigas) physiology, reproduction and next-generation. J Hazard Mater. 2024;480:135742. |
Crassostrea gigas |
rnaseq |
gill |
adult |
pollutant_exposure |
metabolic_resilience |
stress_response |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 18 day-41 gill libraries (124,984,054 single-end reads) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates 37.3-53.1% and similar across arms (control 45.7%, leachate 46.9%, tire particles 43.8%). Expressed-SNP allele frequencies at 80 sites (few, because reads are 76 bp) show every library is a different oyster (all pairs differ by 0.213 or more against 0.037 for one RNA resequenced). No library is an outlier (median VST correlations 0.87-0.90). ~ condition (6 v 6): 46 of 15,278 tested genes reach FDR < 0.05 (26 higher, 20 lower with high leachate); PC1 explains 21.5% of variance. Higher are innate RNA-sensing and antiviral genes (double-stranded RNA-specific adenosine deaminase, HELZ2-like exoribonuclease), acyl-CoA desaturase and agmatinase, consistent with the publication’s activation of stress responses and energy metabolism under leachate; the small number of genes agrees with its conclusion of limited effects in adults. |
| CGIG_TIREPARTICLE_RNASEQ_PRJNA856813 |
10.1016/j.jhazmat.2024.135742 |
Bernardini I, Tallec K, Paul-Pont I, Peruzza L, Dalla Rovere G, Huber M, Di Poi C, Koechlin H, Quere C, Quillien V, Le Grand J, Le Goic N, Lambert C, Lagarde F, Detree C, Trevisan R, Corporeau C, Patarnello T, Milan M, Huvet A. Effects of tire particles and associated-chemicals on the Pacific oyster (Magallana gigas) physiology, reproduction and next-generation. J Hazard Mater. 2024;480:135742. |
Crassostrea gigas |
rnaseq |
gill |
adult |
pollutant_exposure |
metabolic_resilience |
stress_response |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 18 day-41 gill libraries (124,984,054 single-end reads) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates 37.3-53.1% and similar across arms (control 45.7%, leachate 46.9%, tire particles 43.8%). Expressed-SNP allele frequencies at 80 sites (few, because reads are 76 bp) show every library is a different oyster (all pairs differ by 0.213 or more against 0.037 for one RNA resequenced). No library is an outlier (median VST correlations 0.87-0.90). ~ condition (6 v 6): 8 of 15,141 tested genes reach FDR < 0.05 (5 higher, 3 lower with high tire particles), among them an ankyrin-like gene and baculoviral IAP repeat-containing protein 8; PC1 explains 14.8% of variance. The near-null response agrees with the publication, which reports transcriptional effects mainly for leachate. |
| CGIG_VCRASSOSTREAE_RNASEQ_PRJNA515169 |
10.1073/pnas.1905747116 |
Rubio T, Oyanedel D, Labreuche Y, Toulza E, Luo X, Bruto M, Chaparro C, Torres M, de Lorgeril J, Haffner P, Vidal-Dupiol J, Lagorce A, Petton B, Mitta G, Jacq A, Le Roux F, Charriere GM, Destoumieux-Garzon D. Species-specific mechanisms of cytotoxicity toward immune cells determine the successful outcome of Vibrio infections. Proc Natl Acad Sci U S A. 2019;116(28):14238-14247. |
Crassostrea gigas |
rnaseq |
whole_organism |
spat |
pathogen_challenge |
immune_responsiveness |
disease_associated |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 9 pooled libraries (223,876,435 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; four runs from ENA FASTQs that match the manifest MD5s and five from NCBI .sra archives that match NCBI’s MD5s, converted with read counts checked against SRA. Mapping rates are 71.4-74.7% and flat across arms. Expressed-SNP allele frequencies at 2,126 sites show the pools are independent samples of one population: every pair differs by 0.074-0.100 against 0.056 for one RNA resequenced, with no closer similarity within an experiment (0.086 within, 0.085 between), so the experiment block absorbs non-genetic batch effects. ~ experiment + condition (3 v 3): 559 of 24,134 tested genes reach FDR < 0.05 (453 higher, 106 lower with J2-9); PC1 explains 63.3% of variance. The two virulent strains elicit a shared response: all 416 genes significant for both change in the same direction and log2 fold changes correlate 0.76. The top genes form an antibacterial inflammatory programme (interleukin 17-like, TNF receptor superfamily member 11A, Toll-like receptors, prostaglandin E2 receptor EP4, serum amyloid A, baculoviral IAP repeat proteins, coadhesin) with no interferon-pathway response, in line with the publication’s finding that all strains are recognized by the immune system; it reports 331 genes against mock across the four strains. |
| CGIG_VTASMANIENSIS_RNASEQ_PRJNA515169 |
10.1073/pnas.1905747116 |
Rubio T, Oyanedel D, Labreuche Y, Toulza E, Luo X, Bruto M, Chaparro C, Torres M, de Lorgeril J, Haffner P, Vidal-Dupiol J, Lagorce A, Petton B, Mitta G, Jacq A, Le Roux F, Charriere GM, Destoumieux-Garzon D. Species-specific mechanisms of cytotoxicity toward immune cells determine the successful outcome of Vibrio infections. Proc Natl Acad Sci U S A. 2019;116(28):14238-14247. |
Crassostrea gigas |
rnaseq |
whole_organism |
spat |
pathogen_challenge |
immune_responsiveness |
disease_associated |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 9 pooled libraries (223,876,435 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06; four runs from ENA FASTQs that match the manifest MD5s and five from NCBI .sra archives that match NCBI’s MD5s, converted with read counts checked against SRA. Mapping rates are 71.4-74.7% and flat across arms. Expressed-SNP allele frequencies at 2,126 sites show the pools are independent samples of one population: every pair differs by 0.074-0.100 against 0.056 for one RNA resequenced, with no closer similarity within an experiment (0.086 within, 0.085 between), so the experiment block absorbs non-genetic batch effects. ~ experiment + condition (3 v 3): 489 of 23,984 tested genes reach FDR < 0.05 (397 higher, 92 lower with LGP32); PC1 explains 61.7% of variance. The two virulent strains elicit a shared response: all 416 genes significant for both change in the same direction and log2 fold changes correlate 0.76. The top genes form an antibacterial inflammatory programme (interleukin 17-like, TNF receptor superfamily member 11A, Toll-like receptors, prostaglandin E2 receptor EP4, serum amyloid A, baculoviral IAP repeat proteins, coadhesin) with no interferon-pathway response, in line with the publication’s finding that all strains are recognized by the immune system; it reports 331 genes against mock across the four strains. |
| CGIG_HEAT6H_RNASEQ_PRJNA407831 |
10.3389/fphys.2018.00825 |
Li A, Li L, Wang W, Song K, Zhang G. Transcriptomics and fitness data reveal adaptive plasticity of thermal tolerance in oysters inhabiting different tidal zones. Front Physiol. 2018;9:825. |
Crassostrea gigas |
rnaseq |
gill |
adult |
temperature |
thermal_tolerance |
stress_response |
23 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 36 pooled gill libraries (573,193,161 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates 65.5-73.8% (median 72.0%; 0 h 70.7%, 6 h 72.4%, 24 h 72.4%). Expressed-SNP allele frequencies at 1,464 sites show no resequenced RNA: pools within a population and time differ by 0.108 or more (mean 0.170) against 0.044 for one RNA resequenced, and pools are closer within a population (0.171) than between populations (0.202), the genetic structure that the population block absorbs. h0_LTJ_2 is an outlier (median VST correlation 0.906-0.908 against a cut-off of 0.957) and is left out; it is the library the publication discarded (LT-I_0h_2), which ties LTJ to the Laoting intertidal population. ~ population + condition (11 v 12): 935 of 23,666 tested genes reach FDR < 0.05 (537 higher, 398 lower at 6 h); the tank-paired model gives 664, all significant genes keep their direction and log2 fold changes correlate 0.925. Heat shock protein 68 genes rise up to log2FC 7.5 with BAG3, while the ER membrane sensor NFE2L1 falls; 11 of 13 significant heat shock protein genes are higher. |
| CGIG_HEAT24H_RNASEQ_PRJNA407831 |
10.3389/fphys.2018.00825 |
Li A, Li L, Wang W, Song K, Zhang G. Transcriptomics and fitness data reveal adaptive plasticity of thermal tolerance in oysters inhabiting different tidal zones. Front Physiol. 2018;9:825. |
Crassostrea gigas |
rnaseq |
gill |
adult |
temperature |
thermal_tolerance |
stress_response |
23 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 36 pooled gill libraries (573,193,161 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates 65.5-73.8% (median 72.0%; 0 h 70.7%, 6 h 72.4%, 24 h 72.4%). Expressed-SNP allele frequencies at 1,464 sites show no resequenced RNA: pools within a population and time differ by 0.108 or more (mean 0.170) against 0.044 for one RNA resequenced, and pools are closer within a population (0.171) than between populations (0.202), the genetic structure that the population block absorbs. h0_LTJ_2 is an outlier (median VST correlation 0.906-0.908 against a cut-off of 0.957) and is left out; it is the library the publication discarded (LT-I_0h_2), which ties LTJ to the Laoting intertidal population. ~ population + condition (11 v 12): 2,714 of 23,282 tested genes reach FDR < 0.05 (1,363 higher, 1,351 lower at 24 h); the tank-paired model gives 2,058, all significant genes keep their direction and log2 fold changes correlate 0.913. Heat shock protein 68 genes (log2FC up to 7.6), BAG3 and alpha-crystallin remain high, and the response broadens from 6 h, consistent with the publication’s delayed large-scale plasticity; 434 genes are significant at both 6 and 24 h. |
| CGIG_LARVAL_OA_RNASEQ_PRJNA298285 |
nan |
University of Brest. RNA-seq of Pacific oyster Crassostrea gigas larvae (trochophore, early and late veliger) reared under two pH and two temperature levels. NCBI BioProject PRJNA298285; public 2015. No linked publication identified. |
Crassostrea gigas |
rnaseq |
whole_organism |
larva |
ocean_acidification_pH |
acidification_tolerance |
environmental_exposure |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 24 larval libraries (598,102,958 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates are low and variable for whole larvae (29.2-56.8%, median 48.4%; ambient 49.1%, acidified 44.8%, warmed 49.6%, acidified + warmed 46.4%). Expressed-SNP allele frequencies at 898 sites show every library is a pool from one larval cohort: all pairs lie within about 0.01-0.03 of same-RNA noise, so treatment is not confounded with parentage. The A and B libraries of a cell are no closer genetically than libraries of other treatments at the same stage (excess over noise 0.008 against 0.0085), so there is no sign of resequenced RNA, but pools of one cohort cannot show whether A and B are separate cultures; their expression profiles are nearly identical, so they may be subsamples of one culture. Allele frequencies diverge more between stages than within (excess 0.017 against 0.0085), consistent with selection or allele-specific expression during development. PC1 (77-81% of variance) is developmental stage. Acidified larvae show no developmental shift along PC1 (trochophore -34.3 against -34.5, early veliger 8.3 against 5.6, late veliger 27.4 against 27.6). ~ stage + condition (6 v 6): 38 of 19,723 tested genes reach FDR < 0.05 (25 higher, 13 lower at pH 7.9), with small effects ( |
| CGIG_LARVAL_HEAT_RNASEQ_PRJNA298285 |
nan |
University of Brest. RNA-seq of Pacific oyster Crassostrea gigas larvae (trochophore, early and late veliger) reared under two pH and two temperature levels. NCBI BioProject PRJNA298285; public 2015. No linked publication identified. |
Crassostrea gigas |
rnaseq |
whole_organism |
larva |
temperature |
thermal_tolerance |
environmental_exposure |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_complete_not_harmonized |
All 24 larval libraries (598,102,958 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates are low and variable for whole larvae (29.2-56.8%, median 48.4%; ambient 49.1%, acidified 44.8%, warmed 49.6%, acidified + warmed 46.4%). Expressed-SNP allele frequencies at 898 sites show every library is a pool from one larval cohort: all pairs lie within about 0.01-0.03 of same-RNA noise, so treatment is not confounded with parentage. The A and B libraries of a cell are no closer genetically than libraries of other treatments at the same stage (excess over noise 0.008 against 0.0085), so there is no sign of resequenced RNA, but pools of one cohort cannot show whether A and B are separate cultures; their expression profiles are nearly identical, so they may be subsamples of one culture. Allele frequencies diverge more between stages than within (excess 0.017 against 0.0085), consistent with selection or allele-specific expression during development. PC1 (77-81% of variance) is developmental stage. Warmed larvae are developmentally ahead of ambient larvae of the same age: on PC1 the early veligers move from -6.8 to 22.2 (about 70% of the way to the late-veliger profile at 35.0), with smaller shifts at the trochophore (-49.8 to -40.8) and late veliger (35.0 to 40.1) stages. ~ stage + condition (6 v 6) gives 3,295 of 19,864 tested genes at FDR < 0.05, but most reflect developmental stage rather than a thermal response, and with two libraries per cell developmental progress cannot be modelled separately, so the record is not harmonized. |
| CGIG_LARVAL_MULTISTRESS_RNASEQ_PRJNA298285 |
nan |
University of Brest. RNA-seq of Pacific oyster Crassostrea gigas larvae (trochophore, early and late veliger) reared under two pH and two temperature levels. NCBI BioProject PRJNA298285; public 2015. No linked publication identified. |
Crassostrea gigas |
rnaseq |
whole_organism |
larva |
multi_stressor_exposure |
larval_viability |
environmental_exposure |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_complete_not_harmonized |
All 24 larval libraries (598,102,958 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates are low and variable for whole larvae (29.2-56.8%, median 48.4%; ambient 49.1%, acidified 44.8%, warmed 49.6%, acidified + warmed 46.4%). Expressed-SNP allele frequencies at 898 sites show every library is a pool from one larval cohort: all pairs lie within about 0.01-0.03 of same-RNA noise, so treatment is not confounded with parentage. The A and B libraries of a cell are no closer genetically than libraries of other treatments at the same stage (excess over noise 0.008 against 0.0085), so there is no sign of resequenced RNA, but pools of one cohort cannot show whether A and B are separate cultures; their expression profiles are nearly identical, so they may be subsamples of one culture. Allele frequencies diverge more between stages than within (excess 0.017 against 0.0085), consistent with selection or allele-specific expression during development. PC1 (77-81% of variance) is developmental stage. Warmed larvae are developmentally ahead of ambient larvae of the same age: on PC1 the early veligers move from -6.8 to 22.2 (about 70% of the way to the late-veliger profile at 35.0), with smaller shifts at the trochophore (-49.8 to -40.8) and late veliger (35.0 to 40.1) stages. ~ stage + condition (6 v 6) gives 3,925 of 19,732 tested genes at FDR < 0.05, but most reflect developmental stage rather than a thermal response, and with two libraries per cell developmental progress cannot be modelled separately, so the record is not harmonized. |
| CGIG_PESTO_F0_RNASEQ_PRJEB58194 |
10.1016/j.envpol.2023.121472 |
Sol Dourdin T, Riviere G, Cormier A, Di Poi C, Guyomard K, Rabiller M, Akcha F, Bah Sadialiou T, Le Monier P, Sussarellu R. Molecular and phenotypic effects of early exposure to an environmentally relevant pesticide mixture in the Pacific oyster, Crassostrea gigas. Environ Pollut. 2023;326:121472. |
Crassostrea gigas |
rnaseq |
whole_organism |
embryo_larva |
pollutant_exposure |
larval_viability |
environmental_exposure |
36 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 36 F0 libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 52.8% in controls and 50.3% in exposed pools on average (31.7-65.6% across the 54 PESTO libraries). Expressed-SNP allele frequencies at 460 sites show the F0 pools come from one cohort: control and exposed pools at the same stage differ no more than pools of one treatment (excess over same-RNA noise 0.0165 against 0.0158), so exposure is not confounded with parentage, and no pair is resequenced RNA; the two runs sharing the title BT2Ed are different pools (excess 0.0138). Allele frequencies diverge more between stages (excess 0.032), as in other larval studies. PC1 (96%) is developmental stage. ~ stage + condition (18 v 18): 644 of 21,104 tested genes reach FDR < 0.05 (255 higher, 389 lower with the mixture); adding the F0 group digit as a block gives 642 (566 shared, 643 of 644 same direction, log2FC r = 0.905). Three group-3 control D larvae are the least correlated libraries, a group effect absorbed by that sensitivity model. The response includes five homeobox genes (engrailed-1-B lower), M-phase inducer phosphatase (cdc25) higher and seven cytochrome P450 genes lower, matching the publication’s development-related genes (Hox orthologues, cell-cycle regulators). |
| CGIG_PESTO_F1DIRECT_RNASEQ_PRJEB58194 |
10.1021/acs.est.3c08201 |
Sol Dourdin T, Guyomard K, Rabiller M, Houssais N, Cormier A, Le Monier P, Sussarellu R, Riviere G. Ancestors’ gift: parental early exposure to the environmentally realistic pesticide mixture drives offspring phenotype in a larger extent than direct exposure in the Pacific oyster, Crassostrea gigas. Environ Sci Technol. 2024;58(4):1865-1876. |
Crassostrea gigas |
rnaseq |
whole_organism |
embryo_larva |
pollutant_exposure |
larval_viability |
environmental_exposure |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 12 libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 42.0% in TT and 47.2% in TE pools on average. Expressed-SNP allele frequencies at 310 sites show TE and TT pools are genetically equivalent (excess over same-RNA noise 0.0131 between against 0.0144 within, same stage), as expected for offspring of the same parents, with no resequenced RNA. PC1 (99%) is developmental stage. ~ stage + condition (6 v 6): 17 of 24,306 tested genes reach FDR < 0.05 (1 higher, 16 lower with direct exposure), a near-null response that agrees with the publication’s finding that direct exposure affects the F1 phenotype less than parental exposure. |
| CGIG_PESTO_F1PARENTAL_RNASEQ_PRJEB58194 |
10.1021/acs.est.3c08201 |
Sol Dourdin T, Guyomard K, Rabiller M, Houssais N, Cormier A, Le Monier P, Sussarellu R, Riviere G. Ancestors’ gift: parental early exposure to the environmentally realistic pesticide mixture drives offspring phenotype in a larger extent than direct exposure in the Pacific oyster, Crassostrea gigas. Environ Sci Technol. 2024;58(4):1865-1876. |
Crassostrea gigas |
rnaseq |
whole_organism |
embryo_larva |
pollutant_exposure |
larval_viability |
environmental_exposure |
12 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_complete_not_harmonized |
All 12 libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 42.0% in TT and 43.8% in ET pools on average. Expressed-SNP allele frequencies at 295 sites show ET and TT pools are genetically distinct: they differ 3.6 times more than pools of one group (excess over same-RNA noise 0.058 against 0.016 at the same stage), because offspring of exposed and of control F0 parents necessarily have different parents. ~ stage + condition (6 v 6) gives 307 of 24,153 genes at FDR < 0.05, led by CD109 antigen-like genes (log2FC -5 to -6) whose very large changes are typical of lineage presence-absence variation, so parental exposure cannot be separated from parentage and the record is not harmonized. |
| CGIG_HEAT37_RNASEQ_PRJNA1511593 |
nan |
Chinese Academy of Sciences. Gill transcriptomes of Pacific oyster (Magallana gigas) and a backcross Crassostrea line under control and heat conditions. NCBI BioProject PRJNA1511593; public 2026. No linked publication identified. |
Crassostrea gigas |
rnaseq |
gill |
adult |
temperature |
thermal_tolerance |
stress_response |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_complete_not_harmonized |
All 9 GG gill libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 68.7-69.5% by group. The sample-name reading is confirmed by heat-shock induction: heat shock protein 68 genes rise up to log2FC 10.6 at 37 C for 12 h and 8.5 at 42 C for 1 h, with BAG3 and the Hsp90 co-chaperone Cdc37. Expressed-SNP allele frequencies at 2,523 sites show every library is a pool and that the three groups are genetically distinct (mean difference 0.187 between groups against 0.072 within, 0.049-0.052 expected for one RNA resequenced), so heat is confounded with genetic background; the modest excess within groups also leaves open that a group’s three pools are subsamples of one batch. ~ condition (3 v 3) gives 7,865 of 21,508 tested genes at FDR < 0.05 (37%), a count inflated by the genetic difference between groups, so the record is not harmonized. |
| CGIG_HEAT42_RNASEQ_PRJNA1511593 |
nan |
Chinese Academy of Sciences. Gill transcriptomes of Pacific oyster (Magallana gigas) and a backcross Crassostrea line under control and heat conditions. NCBI BioProject PRJNA1511593; public 2026. No linked publication identified. |
Crassostrea gigas |
rnaseq |
gill |
adult |
temperature |
thermal_tolerance |
stress_response |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_complete_not_harmonized |
All 9 GG gill libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 68.7-69.5% by group. The sample-name reading is confirmed by heat-shock induction: heat shock protein 68 genes rise up to log2FC 10.6 at 37 C for 12 h and 8.5 at 42 C for 1 h, with BAG3 and the Hsp90 co-chaperone Cdc37. Expressed-SNP allele frequencies at 2,523 sites show every library is a pool and that the three groups are genetically distinct (mean difference 0.187 between groups against 0.072 within, 0.049-0.052 expected for one RNA resequenced), so heat is confounded with genetic background; the modest excess within groups also leaves open that a group’s three pools are subsamples of one batch. ~ condition (3 v 3) gives 14,382 of 21,576 tested genes at FDR < 0.05 (67%), a count inflated by the genetic difference between groups, so the record is not harmonized. |
| CGIG_VIBRIO12H_RNASEQ_PRJNA852380 |
nan |
Zhejiang Wanli University. Vibrio stress of the Pacific oyster (digestive gland RNA-seq time course). NCBI BioProject PRJNA852380; submitted 2022, public 2026. No linked publication confirmed; possibly the Vibrio dataset of Liu Y, Bao Z, Lin Z, Xue Q. Fish Shellfish Immunol. 2022;131:1027-1039 (doi:10.1016/j.fsi.2022.11.009). |
Crassostrea gigas |
rnaseq |
digestive_gland |
juvenile |
pathogen_challenge |
immune_responsiveness |
disease_associated |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 18 digestive-gland libraries (426,745,884 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 74.8-77.4% and flat across groups. Expressed-SNP allele frequencies at 2,640 sites show all libraries are independent pools from one population: pools differ as much within a group as between groups (0.189 against 0.190, 0.046 for one RNA resequenced), so time is not confounded with genetic background. The response builds over time (85, 138, 236, 1,233 and 3,296 genes at FDR < 0.05 at 1, 3, 6, 12 and 24 h); the 1-6 h contrasts are not harmonized, to avoid several correlated records on one control set. ~ condition (3 v 3): 1,233 of 20,757 tested genes reach FDR < 0.05 (859 higher, 374 lower at 12 h); PC1 explains 41.4% of variance. The top genes form an antibacterial programme (TNF receptor, MyD88, prostaglandin E2 receptor EP4, Toll-like receptors) that replicates the independent PRJNA515169 Vibrio records: 225 genes are significant in both this record and the V. crassostreae J2-9 record, 223 of them in the same direction (207 of 208 for V. tasmaniensis LGP32), with log2 fold changes correlated 0.33-0.35 across about 15,000 genes. |
| CGIG_VIBRIO24H_RNASEQ_PRJNA852380 |
nan |
Zhejiang Wanli University. Vibrio stress of the Pacific oyster (digestive gland RNA-seq time course). NCBI BioProject PRJNA852380; submitted 2022, public 2026. No linked publication confirmed; possibly the Vibrio dataset of Liu Y, Bao Z, Lin Z, Xue Q. Fish Shellfish Immunol. 2022;131:1027-1039 (doi:10.1016/j.fsi.2022.11.009). |
Crassostrea gigas |
rnaseq |
digestive_gland |
juvenile |
pathogen_challenge |
immune_responsiveness |
disease_associated |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_harmonized |
All 18 digestive-gland libraries (426,745,884 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 74.8-77.4% and flat across groups. Expressed-SNP allele frequencies at 2,640 sites show all libraries are independent pools from one population: pools differ as much within a group as between groups (0.189 against 0.190, 0.046 for one RNA resequenced), so time is not confounded with genetic background. The response builds over time (85, 138, 236, 1,233 and 3,296 genes at FDR < 0.05 at 1, 3, 6, 12 and 24 h); the 1-6 h contrasts are not harmonized, to avoid several correlated records on one control set. ~ condition (3 v 3): 3,296 of 20,792 tested genes reach FDR < 0.05 (1,816 higher, 1,480 lower at 24 h); PC1 explains 51.0% of variance. The response broadens beyond the 12 h antibacterial programme (25 heat shock protein genes significant, superoxide dismutase [Cu-Zn] lower), and agreement with the PRJNA515169 Vibrio records is weaker (about 95% of shared significant genes in the same direction; log2FC r = 0.14-0.18), consistent with a later systemic stage. |
| CGIG_HEAT12H_RNASEQ_PRJNA1244231 |
nan |
Chinese Academy of Sciences. Magallana gigas transcriptome or gene expression (role of ERK kinase in thermal adaptation). NCBI BioProject PRJNA1244231; registered 2025. No linked publication identified. |
Crassostrea gigas |
rnaseq |
gill |
adult |
temperature |
thermal_tolerance |
stress_response |
6 |
public_raw_aree_reanalysis_complete |
raw_reanalysis_complete_not_harmonized |
All 12 gill libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 70.7-73.2%. The sample-name reading is supported by heat-shock induction: summed heat shock protein 70 TPM rises 3.4-fold from 0 h to 12 h in seawater-injected oysters (2.1-fold with the ERK inhibitor), with individual HSP70 genes up to log2FC 9.2. Expressed-SNP allele frequencies at 3,136 sites show that the three libraries within each group are indistinguishable from one RNA resequenced (mean difference 0.053 within groups against 0.051 expected, correlation 0.92) while groups are genetically distinct pools (0.178 between groups); summed HSP70 TPM also differs by under 1% between libraries within a group. ~ condition (3 v 3) gives 12,303 of 23,144 tested genes at FDR < 0.05 (53%), a count driven by technical replication and the genetic difference between pools, so the record is not harmonized. |