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Sample GSM2340129 Query DataSets for GSM2340129
Status Public on Oct 09, 2019
Title Mutant rep 3
Sample type SRA
Source name pig embryo at 17.5-18.0 dpc
Organism Sus scrofa
Characteristics breed: Large White
genotype: homozygous for the two QTNs (QQ)
tissue: embryo
developmental stage: 17.5-18 dpc
Extracted molecule total RNA
Extraction protocol Embryos were harvested from the uterus and stored in liquid nitrogen for RNA extraction. The extra-embryonic tissues of each embryo were collected for DNA extraction and genotyping of the VRTN QTNs. Total RNA was isolated from three wild-type (qq) and three mutant (QQ) pig embryos using Trizol reagent, which was then used to construct cDNA libraries using the TruSeq RNA Sample Preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Trimmed, clean reads were mapped to the pig reference genome (Sscrofa 10.2) using the SOAP2 software and allowing five mismatches(Li et al., 2009).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol (Mortazavi et al., 2008). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
A FDR of no more than 0.001 (FDR ≤ 0.001) and a difference ratio of the RPKM between the wild-type and mutant samples of no less than 1 (|log2 ratio| ≥ 1) were adopted as the significance thresholds to identify DEGs.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: txt files include RPKM values for each Sample.
Submission date Oct 09, 2016
Last update date Oct 09, 2019
Contact name Yanyu Dean
Phone 86-791-83813080
Organization name Jiangxi Agricultural University
Lab State Key Laboratory of Pig Genetic Improvement and Production Technology
Street address Lushanzhong888, Changbei district
City Nanchang
ZIP/Postal code 330044
Country China
Platform ID GPL11429
Series (2)
GSE87775 VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development [RNA-seq]
GSE87776 VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development
BioSample SAMN05891562
SRA SRX2234305

Supplementary file Size Download File type/resource
GSM2340129_QQ-3.txt.gz 360.7 Kb (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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