|
| Status |
Public on Jan 15, 2015 |
| Title |
1_SusScrofa |
| Sample type |
SRA |
| |
|
| Source name |
subcuteneous adipose tissue
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: subcuteneous adipose
biological_state: Low
Sex: f
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy lipid Mini kit
TruSeq RNA Sample Prep (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Alignment: STAR
Filtering: SAM flag 1792 (not primary alignment, read fails platform/vendor quality checks, read is PCR or optical duplicate)
Count reads: HTSeq
Library size factor estimation: DESeq
Normalization of reads: voom (limma), samples were corrected for gender
Filter of reads with expression lower than 5
Genome_build: SScrofa10.2.72
Supplementary_files_format_and_content: comma seperated files with raw and normalized counts
|
| |
|
| Submission date |
Sep 09, 2014 |
| Last update date |
May 15, 2019 |
| 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 |
GPL19176 |
| Series (1) |
| GSE61271 |
RNA-Sequencing of lean, intermediate, and obese pigs |
|
| Relations |
| SRA |
SRX698199 |
| BioSample |
SAMN03031512 |
