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Sample GSM653223 Query DataSets for GSM653223
Status Public on Jan 12, 2011
Title 2270 LI, mRNA
Sample type SRA
 
Source name liver
Organism Sus scrofa
Characteristics breed: White Duroc × Erhualian
generation: F2
gender: female
age: 240 days
tissue: liver
sib: 2270
Treatment protocol All samples were put into liquid nitrogen within 30 min after slaughtering, and then conserved in a -80oC ultra freezer until RNA extraction.
Growth protocol All animals were housed in the same environmental conditions and had a good body condition. The room temperatures were uncontrolled with natural lighting. Animals were floor fed three times a day.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions. Remaining DNA was removed with RNase-free DNase I (New England Biolabs) for 30 min at 37oC. The quality of total RNA was assessed by the 2100 Bioanalyzer (Agilent) and agarose gel electrophoresis. We isolated poly (A) mRNA from the total RNA samples with oligo (dT) magnetic beads (Invitrogen). Purified mRNA was first fragmented by the RNA fragmentation kit (Ambion). The first-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase (Invitrogen), and the second-strand cDNA was synthesized using RNase H (Invitrogen) and DNA polymerase (New England Biolabs).
The cDNA libraries were prepared using the Illumina Genomic DNA Sample Prep kit (Illumina) in accordance with the manufacturer’s protocol and loaded onto flow cell channels of the Illumina HiSeq 2000 platform for paired-end 90 bp × 2 sequencing. The average insert size for the paired-end libraries was 200 bp (from 180 to 220 bp).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Leaf fat weight: 977.5 g
Veil fat weight: 830 g
Abdominal fat weight: 980 g
Body weight at day: 68.7 kg
Shoulder fat thickness: 3.06 mm
Waist fat thickness: 1.882 mm

Understanding the complexity of the pig transcriptome.
Data processing Sequence reads were obtained and filtered using the Illumina Genome Analyzer Pipeline. The following reads were filtered: those with more than half of the base's qualities <5, those containing >5 Ns, and those containing adapters.

Reads were mapped to the reference genome (Sscrofa9.2) by SOAP2 (Li et al. 2009) to analyze their expression and distribution on the genome.
 
Submission date Jan 11, 2011
Last update date May 15, 2019
Contact name Lusheng Huang
E-mail(s) Lushenghuang@hotmail.com
Organization name Jiangxi Agricultural University
Lab Key Laboratory for Animal Biotechnology of Jiangxi Province
Street address No. 1101, Zhimin Avenue
City Nanchang
State/province Jiangxi Province
ZIP/Postal code 330045
Country China
 
Platform ID GPL11429
Series (2)
GSE26382 A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)
GSE26572 A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing
Relations
SRA SRX054585
BioSample SAMN00254170

Supplementary file Size Download File type/resource
GSM653223_2270LI.PosCoverage.txt.gz 393.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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