|
| 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 |
| E-mail(s) |
yanyuduan@gmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN05891562 |
| SRA |
SRX2234305 |
