Can’t remember where it was discussed (probably lab meeting), but I created a GitHub Issue to add all of geoduck RNAseq data to NCBI Short Read Archive (SRA). Anyway, got all the remaining RNAseq data uploaded to the NCBI SRA and organized into the correct BioSamples and BioProjects.
The table below has links to each corresponding NCBI BioSample and BioProject. NCBI indicates that references should point to a particular BioProject; not individual Short Read References (SRR).
I’ve added the corresponding links to the NCBI BioProjects to our sequencing database, Nightingales (Google Sheet).
Below is a table sorted by BioProject that also includes links to each BioSample for each “SeqID” (the SeqID is a unique identifier, usually the FastQ filename prefix) used in Nightingales (Google Sheet).
| SeqID | BioSample | Tissue | BioProject |
|---|---|---|---|
| Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-larvae-day5-RNA-EPI-99-2_S16_L002_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-larvae-day5-RNA-EPI-99-6_S48_L006_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-larvae-day5-RNA-EPI-99-7_S56_L007_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_001 | 11259647 | larvae | PRJNA529226 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-1_S6_L001_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-3_S22_L003_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-4_S30_L004_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_001 | 15517238 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-1_S7_L001_001 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_001 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_001 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_001 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_001 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-6_S47_L006_001 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_001 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_001 | 15517239 | juvenile | PRJNA566166 |
| NR005_S4_L001_001 | 15517237 | juvenile | PRJNA566166 |
| NR005_S4_L002_001 | 15517237 | juvenile | PRJNA566166 |
| NR019_S7_L001_001 | 15517239 | juvenile | PRJNA566166 |
| NR019_S7_L002_001 | 15517239 | juvenile | PRJNA566166 |
| Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001 | 15517237 | juvenile | PRJNA566166 |
| Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002 | 15517237 | juvenile | PRJNA566166 |
| Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001 | 15517239 | juvenile | PRJNA566166 |
| Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L002 | 15517239 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-2_S12_L002_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-4_S28_L004_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-7_S52_L007_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-115-8_S60_L008_001 | 15517236 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-1_S5_L001_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-2_S13_L002_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-7_S53_L007_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-juvenile-OA-exposure-RNA-EPI-116-8_S61_L008_001 | 15517237 | juvenile | PRJNA566166 |
| Geoduck-ctenidia-RNA-1_S3_L001_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-ctenidia-RNA-2_S11_L002_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-ctenidia-RNA-3_S19_L003_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-ctenidia-RNA-4_S27_L004_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-ctenidia-RNA-5_S35_L005_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-ctenidia-RNA-6_S43_L006_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-ctenidia-RNA-7_S51_L007_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-ctenidia-RNA-8_S59_L008_001 | 15524251 | ctenidia | PRJNA646071 |
| Geoduck-gonad-RNA-1_S1_L001_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-gonad-RNA-2_S9_L002_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-gonad-RNA-3_S17_L003_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-gonad-RNA-4_S25_L004_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-gonad-RNA-5_S33_L005_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-gonad-RNA-6_S41_L006_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-gonad-RNA-7_S49_L007_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-gonad-RNA-8_S57_L008_001 | 15524260 | gonad | PRJNA646071 |
| Geoduck-heart-RNA-1_S2_L001_001 | 15524261 | heart | PRJNA646071 |
| Geoduck-heart-RNA-2_S10_L002_001 | 15524261 | heart | PRJNA646071 |
| Geoduck-heart-RNA-3_S18_L003_001 | 15524261 | heart | PRJNA646071 |
| Geoduck-heart-RNA-4_S26_L004_001 | 15524261 | heart | PRJNA646071 |
| Geoduck-heart-RNA-5_S34_L005_001 | 15524261 | heart | PRJNA646071 |
| Geoduck-heart-RNA-6_S42_L006_001 | 15524261 | heart | PRJNA646071 |
| Geoduck-heart-RNA-7_S50_L007_001 | 15524261 | heart | PRJNA646071 |
| Geoduck-heart-RNA-8_S58_L008_001 | 15524261 | heart | PRJNA646071 |
| NR006_S3_L001_001 | 15524260 | gonad | PRJNA646071 |
| NR006_S3_L002_001 | 15524260 | gonad | PRJNA646071 |
| NR012_S1_L001_001 | 15524251 | ctenidia | PRJNA646071 |
| NR012_S1_L002_001 | 15524251 | ctenidia | PRJNA646071 |
| Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L001 | 15524260 | gonad | PRJNA646071 |
| Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L002 | 15524260 | gonad | PRJNA646071 |
| Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L001 | 15524251 | ctenidia | PRJNA646071 |
| Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002 | 15524251 | ctenidia | PRJNA646071 |