|
| Status |
Public on Feb 09, 2013 |
| Title |
Testis Low androstenone rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
Testis Low androstenone
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Duroc x F2 cross. F2 was created by crossing F1 animals (Leicoma x German Landrace). Large White pig
tissue: testis
age: 116 day old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Testis and liver were frozen in liquid nitrogen immediately after slaughter and stored at -80°C until used for RNA extraction. RNA was harvested using RNeasy Mini Kit according to manufacturer’s recommendations (Qiagen).
Full-length cDNA was obtained from 1 μg of RNA, with the SMART cDNA Library Construction Kit (Clontech, USA), according to the manufacturer's instructions. Libraries of amplified RNA for each sample were prepared following the Illumina mRNA-Seq protocol.
The library preparations were sequenced on an Illumina HiSeq 2000 as single-reads to 100 bp using 1 lane per sample on the same flow-cell (first sequencing run) at GATC Biotech AG (Konstanz, Germany).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample A4
|
| Data processing |
Base calling performed using Illumina Casava 1.7
The raw reads were trimmed for adapter sequences and mapped to sscrofa9 refseq and mRNA sequences and sscrofa9 whole genome using bwa using the default parameteres.
Raw read counts were calculated from the annotated files using samtools using default parameters for sscrofa9 refseq and mrna mapppings using the default parameters.
Genome_build: Sscrofa9 (NCBI)
Supplementary_files_format_and_content: tab limited text file include raw read count for each sample
|
| |
|
| Submission date |
Feb 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sudeeep Sahadevan |
| E-mail(s) |
ssud@itw.uni-bonn.de
|
| Organization name |
University of Bonn
|
| Department |
Institute of Animal Science
|
| Lab |
Animal husbandry and breeding
|
| Street address |
Endenicher Allee 15
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11429 |
| Series (1) |
| GSE44171 |
RNA deep sequencing reveals novel candidate genes and polymorphisms in boar testis and liver tissues with divergent androstenone levels. |
|
| Relations |
| SRA |
SRX229763 |
| BioSample |
SAMN01915394 |
