|
| Status |
Public on Mar 03, 2021 |
| Title |
B10 |
| Sample type |
SRA |
| |
|
| Source name |
Muscle
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Muscle
breed: Bos taurus x Bos indicus
animal: B23
date collected: 201
year: 2
treatment: MOLMET
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration and quality were determined using the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples had RNA integrity number equal or greater than 6.1.
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).
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 |
Mar 02, 2021 |
| Last update date |
Mar 03, 2021 |
| 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) |
| GSE168091 |
Effects of maternal gestational diet, with or without methionine, on muscle transcriptome of Bos indicus-influenced beef calves following a vaccine-induced immunological challenge |
|
| Relations |
| BioSample |
SAMN18114032 |
| SRA |
SRX10208228 |
