 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 15, 2020 |
| Title |
Entry group rep5 (gilt) |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Duroc
group: entry
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from blood samples using the Total RNA Purification Kit (Norgen, Biotek Corp.) following the manufacturer’s protocol. An in-solution DNase I digestion step was employed to remove the contaminant DNA as recommended. RNA was then recovered by the RNeasy MinElute Cleanup kit (Qiagen, Hilden, Germany) and quantified using the Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, USA). The purity and integrity of total RNA were assessed with the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNA samples with integrity number larger than 6.0 were then subjected to a globin depletion protocol to remove the majority of globin transcripts.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Raw reads were aligned to pig reference genome sequence assembly (Sscrofa10.2) using Tophat 2.0.2 with default parameters which included: enable use of GTF file, set minimum anchor length of 8, accept zero mismatches in the anchor region, allow intron length between 50 and 500,000, and allow up to 20 alignments to the reference for a given read. For annotation of genes, we used the GTF file for Sscrofa10.2 from Ensembl version 67
The number of reads uniquely mapped to each gene was determined using Htseq-count (v0.5.3.p3).
Genome_build: Ssc10.2
|
| |
|
| Submission date |
Mar 15, 2017 |
| Last update date |
Mar 15, 2020 |
| Contact name |
Graham Plastow |
| E-mail(s) |
plastow@ualberta.ca
|
| Organization name |
University of Alberta
|
| Street address |
8215 - 112 Street
|
| City |
Edmonton |
| ZIP/Postal code |
T6G 2C8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE96640 |
Transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine-cytokine receptor interaction pathway related to health status |
|
| Relations |
| BioSample |
SAMN06604160 |
| SRA |
SRX2642298 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2537046_10357-72.stats.txt.gz |
98.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
