|
| Status |
Public on Mar 15, 2022 |
| Title |
28d_RNA_replicate_2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Bama pig
tissue: Liver
condition: Developmental stage
age: postnatal day 28
Sex: female
chip antibody: n/a
|
| Treatment protocol |
Six two-years-old female pigs were fed with a high fat diet (15.12 MJ·kg-1 metabolizable energy, 11.26% crude protein, 6.8% fat and 5% lysine) for 22 weeks, compared with the pigs of two-years-old fed with well-characterized normal diet for 22 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
liver were flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.
rRNA depletion protocol (Ribo-Zero kit, Epicentre) and Illumina TruSeq stranded RNA-Seq library protocol are used to construct the RNA-Seq libraries. cDNA libraries were sequenced on HiSeq X Ten (Illumina) platform to produce 150-bp paired-end raw reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
28d_2
all_samples_quant_mRNA.tpm.txt
|
| Data processing |
Sequence reads are aligned to pig reference genome (Sscrofa 11.1) by alignment tool STAR (version 2.6.0c).
The aligned reads of these samples were assembled using Cufflinks (version 2.1.1).
Kallisto (v 0.44.0) was used to quantify gene expression and obtain TPM expression values.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: mRNA expression level (TPM), text file
|
| |
|
| Submission date |
Jun 08, 2021 |
| Last update date |
Mar 15, 2022 |
| Contact name |
Jing Li |
| E-mail(s) |
lijing-jane@foxmail.com
|
| Phone |
+8615882474902
|
| Organization name |
Sichuan Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
No. 211 Huimin Road, Wenjiang District
|
| City |
Chengdu |
| State/province |
China |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE176387 |
Three-dimensional geome study of procine livers during development and metabolic adaptation |
|
| Relations |
| BioSample |
SAMN18317847 |
| SRA |
SRX10588941 |
