|
| Status |
Public on Nov 04, 2014 |
| Title |
SHF1 |
| Sample type |
SRA |
| |
|
| Source name |
Subcutaneous adipose depot
|
| Organism |
Ovis aries |
| Characteristics |
tissue: Subcutaneous adipose depot
gender: Female
developmental stage: fetus
maternal diet: Hay
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples using the RNeasy Mini kit (QIAGEN, Valencia, CA, USA) and then treated with DNase-free DNase Set (QIAGEN) to avoid genomic DNA amplification.
Libraries were prepared following the Illumina mRNA-Seq protocol. Sequencing libraries were created from 50 ng samples and sequenced with Illumina’s HiSeq 2000 at the University of Wisconsin-Madison Biotechnology Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped to the reference genome (Oar_v3.1) using the software package Tophat (v2.0.4).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.1.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.1.1) was used for merging together each of the assemblies with the reference ovine annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty) developed by Simon Anders at EMBL (Heidelberg, Germany).
Genome_build: Sheep genome assembly: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text files including locus, number of mapped reads, gene name, and chromosome location.
|
| |
|
| Submission date |
Nov 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Animal and Dairy Sciences
|
| Street address |
1675 Observatory Drive
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL15670 |
| Series (1) |
| GSE62938 |
Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep |
|
| Relations |
| BioSample |
SAMN03160402 |
| SRA |
SRX750286 |
