|
| Status |
Public on Jun 02, 2021 |
| Title |
202_24h |
| Sample type |
SRA |
| |
|
| Source name |
Longissimus thoracis et lumborum muscle
|
| Organism |
Bos taurus |
| Characteristics |
animal_id: 202
sampling time point: 24h
weight (kg): 558
rna_id: 223
tissue: Longissimus thoracis et lumborum muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Core muscle tissue samples from the longissimus thoracis et lumborum were collected at 5 different time points [0 h (45 min post-mortem), 6 h, 24 h, 48 h, and 72 h (drip cooler)] post-mortem from the left-side carcasses above the grading site , and immediately frozen in liquid nitrogen, and then stored at -80 °C temperature until RNA extraction. The RNA was extracted using Qiagen RNAeasy mini kit (Qiagen N.V., Valenca, CA, United States) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Prep protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed using Trimmomatic v0.39 using default parameters and a minimum length of 36 bp.
Quality control was performed using FastQC v0.11.8. Reads were mapped to the ARS-UCD1.2 bovine genome assembly using STAR v2.7.0f with the following parameters: quantMode GeneCounts.
Read counts were obtained using featureCounts v1.6.4 with the following parameters: -s 0 -p -t exon -g gene_id -a Bos_taurus.ARS-UCD1.2.95.gtf.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The file read_counts_reverse_strand.txt is a tab seperated file that contains the read counts from the reverse strand for all 35 samples.
|
| |
|
| Submission date |
Dec 23, 2020 |
| Last update date |
Jun 02, 2021 |
| Contact name |
Payam Vahmani |
| E-mail(s) |
pvahmani@ucdavis.edu
|
| Organization name |
University of California Davis
|
| Department |
Department of Animal Science
|
| Street address |
One Shields Avenue
|
| City |
Davis |
| State/province |
California |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE163766 |
Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis et lumborum muscle tissue over time post-mortem |
|
| Relations |
| BioSample |
SAMN17145274 |
| SRA |
SRX9722343 |
