|
| Status |
Public on Nov 01, 2013 |
| Title |
HT_Low_2 |
| Sample type |
SRA |
| |
|
| Source name |
hypothalamus, low growth and fatness
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Iberian x Landrace backcross
tissue: hypothalamus
phenotype: low growth and fatness
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RiboPure TM of High Quality total RNA kit.
Paired-end libraries with fragments of 300 bp were prepared using the TrueSeq RNA sample Prep kit v2 (Illumina).
Multiplex sequencing of the libraries was performed on an Illumina HiSeq 2000 with three samples per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA
|
| Data processing |
Illumina Casava software was used for base calling.
FastQC was used to assess the quality of the raw sequencing data.
Trim Galore was used to quality trim the data and remove sequencing adaptors.
Reads were mapped against the reference genome using TopHat v.2.0.5 with Bowtie2.
Transcripts were assembled and quantified in FPKM by Cufflinks v.2.0.2.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Text file with the RPKM normalized expression values of each gene per group (high or low growth and fatness).
|
| |
|
| Submission date |
Oct 31, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dafne Pérez Montarelo |
| Organization name |
INIA
|
| Department |
Animals Genetics
|
| Street address |
Crta. de la Coruña Km 7.5
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11429 |
| Series (1) |
| GSE51968 |
Transcriptome sequencing of porcine hypothalamic samples |
|
| Relations |
| BioSample |
SAMN02389761 |
| SRA |
SRX372019 |
