|
| Status |
Public on Jun 01, 2020 |
| Title |
93 |
| Sample type |
SRA |
| |
|
| Source name |
psoas major muscle
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: psoas major muscle
breed: Danbred_Landrace
rin: 7.7
feed conversion ratio: 2.15
sampling age(days): 154
batch: 5
gender: male
|
| Treatment protocol |
Feed intake and growth was measured from ~28 to ~100kg, and Feed Conversion Ratio and Residual feed intake was calculated
|
| Growth protocol |
Pigs were fed ad libitum until ~100kg
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Muscle tissue samples from the psoas major muscle were collected imediatly post slaughter and preserved RNAlater (Ambion, Austin, Texas). Samples were stored at -25.
All processing from extraction to sequencing was a service provided by BGI: https://www.bgi.com/global/
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Reads were trimmed for quality and artificial sequences using trimmomatic version 0.39, using the default suggested setting for paired end reads: java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36
The read were mapped using STAR aligner version 2.7.1a. We generated and index from the Sus Scrofa genome version 11.1 using Ensembl annotation version 11.1.96 for splice reference. Read were mapped using default setting for paired end reads.
The reads were annotated and quantified to the Sus Scrofa Ensembl annotation version 11.1.96 by including the --quantMode GeneCounts command in the alignment step.
Genome_build: Sus Scrofa 11.1
Supplementary_files_format_and_content: The proceessed files include 4 colums: the first has the Ensembl gene names, the second column included the annotated readcounts assuming no strandedness and the 3rd and 4th columns assuming forward and reverse strand mapping respectively.
|
| |
|
| Submission date |
Apr 18, 2020 |
| Last update date |
Jun 02, 2020 |
| Contact name |
Haja N Kadarmideen |
| E-mail(s) |
[email protected]
|
| Organization name |
Technical University of Denmark
|
| Department |
Department of Applied Mathematics and Computer Science
|
| Lab |
Quantitative Genomics, Bioinformatics & Computational Biology (QBC) Group
|
| Street address |
Richard Petersens Plads, Building 324
|
| City |
Kongens Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL26285 |
| Series (1) |
| GSE148889 |
Genome regulation and gene interaction networks inferred from muscle transcriptome underlying feed efficiency in Pigs |
|
| Relations |
| BioSample |
SAMN14616094 |
| SRA |
SRX8136054 |
