|
| Status |
Public on Mar 07, 2020 |
| Title |
Steer 458 |
| Sample type |
SRA |
| |
|
| Source name |
longissimus dorsi muscle
|
| Organism |
Bos taurus |
| Characteristics |
breed: Hanwoo (Korean cattle)
tissue: longissimus dorsi muscle
age: post natal day 930
sex type: Steer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
longissimus dorsi muscles were removed, flash frozen on liquid nitrogen and dry ice. Total RNAs were isolated using Trizol (invitrogen) and a RNeasy RNA purification kit with DNase treatment (Qiagen). mRNA was isolated from the total RNA using oligo-dT beads and were reverse transcribed into double strand cDNA fragments. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina NextSeq 500 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality of RNA-seq reads was checked using FastQC
The reads passed the quality control were mapped to Bovine Taurus genome (UMD3.1) from UCSC using Tophat2 (v2.0.2)
The reads were counted using HTseq (v0.5.3p3)
Trimmed mean of M values (TMM) were calculated using a protocol from Robinson et al., Genome Biology, 2010.
Genome_build: UMD3.1
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample
|
| |
|
| Submission date |
Mar 07, 2017 |
| Last update date |
Mar 10, 2020 |
| Contact name |
Sang Weon Na |
| E-mail(s) |
kerberosia@snu.ac.kr
|
| Phone |
+82-10-9026-2830
|
| Organization name |
Seoul National University
|
| Department |
College of Agriculture and Life Science
|
| Lab |
Ruminant Nutrition and Physiology labratory
|
| Street address |
1, Gwanak-ro, Gwanak-gu, Seoul-si
|
| City |
Seoul-si |
| State/province |
Seoul-si |
| ZIP/Postal code |
KS013 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE95789 |
Comparison of transcriptome profiles between bulls and steers in the longissimus dorsi muscle of Korean cattle |
|
| Relations |
| BioSample |
SAMN06545937 |
| SRA |
SRX2618486 |
