|
| Status |
Public on Feb 09, 2024 |
| Title |
Whole sac-fry, Low choline, Family E, Sire 2, 14-days post-hatch |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
tissue: Whole organism
strain: NCCCWA breeding program
genotype: ARS-Fp/Fc-R
treatment: Low Choline
time: 14-days post-hatch
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy Minikit (Qiagen).
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
102_S21
|
| Data processing |
Trimmed sequence reads were mapped to GCF_013265735.2_USDA_OmykA_1.1/GCF_013265735.2_USDA_OmykA_1.1_rna.fna.gz using Salmon (v0.14.1) (default parameters for paired end)
Read count extraction and normalization were performed using DESeq2.
Assembly: OmykA_1.1
Supplementary files format and content: Excel worksheet file includes normalized counts for each sample at different comparisons used in the manuscript.
|
| |
|
| Submission date |
Sep 14, 2023 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Peggy Biga |
| Organization name |
University of Alabama at Birmingham
|
| Department |
Biology
|
| Lab |
Biga
|
| Street address |
902 14th Street South
|
| City |
Birmingham |
| State/province |
Alabama |
| ZIP/Postal code |
35205 |
| Country |
USA |
| |
|
| Platform ID |
GPL23004 |
| Series (1) |
| GSE243186 |
Maternal Dietary Choline Levels Cause Transcriptome Shift due to Genotype-by-Diet Interaction in Rainbow Trout (Oncorhynchus mykiss) |
|
| Relations |
| BioSample |
SAMN37390519 |
| SRA |
SRX21775292 |
