|
| Status |
Public on Jun 05, 2020 |
| Title |
AT6 |
| Sample type |
SRA |
| |
|
| Source name |
Adipose
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Adipose
breed: Holstein
treatment: 5-hydroxytryptophan
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Valencia, CA). RNA quantiy and quality were determined using Nanodrop™ (2000/2000c Spectrophotometers, Thermo Scientific). All samples had an A260/280 ratio > 1.8.
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
Transcript models were recontructed from read alignments using Cufflinks software (version 2.2.1).
The tool cuffmerge (Cufflinks) was used for merging together each of the assemblies with the reference bovine 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).
Genome_build: Bovine 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 |
Jun 04, 2020 |
| Last update date |
Jun 05, 2020 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
fpenagarican@wisc.edu
|
| 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 |
GPL26012 |
| Series (1) |
| GSE151781 |
Transcriptomic analysis of adipose and muscle of dairy calves supplemented with 5-hydroxytryptophan |
|
| Relations |
| BioSample |
SAMN15098837 |
| SRA |
SRX8468733 |
