|
| Status |
Public on Aug 11, 2024 |
| Title |
liver, 165d, mnr, female, MUN_LIV_76 [mnr_rna_seq_441] |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Papio anubis |
| Characteristics |
tissue: liver
gender: female
gestation days: 165
treatment: mnr
tissue id: MUN_LIV_76
|
| Treatment protocol |
Control dams were fed ad libitum throughout the study, while 30% feed reduction (based on feed consumed by controls at the same gestation stage and adujsted for body weight) started at 30 dG for MNR dams.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver tissue was snap-frozen in liquid nitrogen immediately after collection and stored at -80ºC until use. Total RNA was isolated using TRIzol reagent.
mRNA was purified from total RNA prior to cDNA synthesis. cDNA libraries were prepared using the mRNA-Seq Sample Preparation Kit (Illumina) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Raw sequences were de-multiplexed using the Illumina Casava v1.8 software.
Prealignment QC was performed using Partek Flow. Sequence reads with Phred scores ≥ Q30 were retained.
Sequence reads were aligned against the olive baboon reference genome (Panu_3.0) using STAR 2.5.3a.
Aligned reads were quantified using an expectation-maximization algorithm in Partek Flow and annotated using the NCBI release 93 gene model.
Assembly: Panu_3.0, GCF_000264685.3
Supplementary files format and content: Matrix table of transcript counts before normalization for all genes in 56 samples.
|
| |
|
| Submission date |
Aug 11, 2022 |
| Last update date |
Aug 11, 2024 |
| Contact name |
Jeannie Chan |
| E-mail(s) |
[email protected]
|
| Organization name |
Wake Forest School of Medicine
|
| Department |
Internal Medicine
|
| Street address |
Medical Center Boulevard
|
| City |
Winston-Salem |
| State/province |
NC |
| ZIP/Postal code |
27157 |
| Country |
USA |
| |
|
| Platform ID |
GPL19164 |
| Series (1) |
| GSE211085 |
Effect of maternal nutrient reduction (MNR) during pregnancy on fetal liver gene expression in baboons (Papio anubis). |
|
| Relations |
| BioSample |
SAMN30273766 |
| SRA |
SRX17036162 |
