|
| Status |
Public on Jul 13, 2018 |
| Title |
6125_CONTROL (rna-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Longissimus dorsi
|
| Organism |
Bos taurus |
| Characteristics |
breed: Brangus-Angus
ID: 6125
treatment: CONTROL
tissue: Longissimus dorsi
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen RNeasy Mini kit. RNA yield and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Libraries from individual samples were sequenced with Illumina's HiSeq 3000 at University of Florida Interdisciplinary Center for Biotechnology Research using 100-pb paired-end sequencing reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4)
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using the software package Hisat2 (version: 2.1.0).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Cow genome assembly: ARS-UCD1.2
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Aug 21, 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 |
GPL21659 |
| Series (2) |
| GSE116974 |
Maternal methionine supplementation alters the epigenome of the offspring [RNA-Seq] |
| GSE117195 |
Maternal methionine supplementation alters the epigenome of the offspring |
|
| Relations |
| BioSample |
SAMN09644890 |
| SRA |
SRX4383627 |
