|
| Status |
Public on Jan 16, 2019 |
| Title |
5613P1L |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Bos taurus |
| Characteristics |
diet: High Concentrate One (860g/kg rolled barley, 60g/kg soya bean meal, 60g/kg molasses, and 20g/kg minerals and vitamins plus restricted grass silage for healthy rumen function).
breed: Holstein Friesian
rfi status: High RFI
|
| Growth protocol |
Charolais (n=90) and Holstein Friesian (n=77) steers were allowed ad libitum access to feed. The type of feed animals were allowed varied depending on experimental phase as outlined in the Samples section.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 50mg of frozen biopsy sample by homogenisation in Trizol using manual disruption. Total RNA was purified using Rneasy plus Universal Kits (Qiagen)
Single-end mRNA-seq libraries were generated using the Illumina TruSeq sample prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA (v1.8)
FastQC (v0.11.5) was used to check read quality
Reads were aligned to the reference genome (UMD3.1) using STAR (v2.5.3a). The STAR command "quantMode GeneCounts" was used to map sequenced fragments to protein coding genes of the Bovine genome, according to the Ensembl release 87.
Raw reads generated by STAR were quantified by DESeq2's (v1.16.1) internal analysis pipeline via the command "DESeq")
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Processed data files are in .csv format.
Supplementary_files_format_and_content: First row contains sample I.D.s, column A contains gene I.D.s in Ensembl format with the number of raw reads that map to each specified gene per sample in the other rows.
|
| |
|
| Submission date |
Mar 06, 2018 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Marc Higgins |
| E-mail(s) |
marcghiggins@gmail.com
|
| Organization name |
NUI Galway
|
| Department |
Discipline of Biochemistry
|
| Street address |
University Road
|
| City |
Galway |
| ZIP/Postal code |
H91 CF50 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL19172 |
| Series (1) |
| GSE111464 |
The effect of breed and diet on the liver transcriptome of beef steers divergent in RFI |
|
| Relations |
| BioSample |
SAMN08639215 |
| SRA |
SRX3768141 |
