|
| Status |
Public on May 31, 2019 |
| Title |
low prolific Erhualian sows 2 |
| Sample type |
SRA |
| |
|
| Source name |
Uterus
|
| Organism |
Sus scrofa |
| Characteristics |
phenotype: low prolific
tissue: Endometrium
strain: Erhualian
parity: 7
Stage: day 12 of gestation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Endometrium were collected, immediately frozen in liquid nitrogen and then stored at −80 °C until RNA was isolated. RNA was harvested using Trizol reagent.
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 |
| |
|
| Description |
normalizeExp.csv
EL2
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa 11.1 whole genome using subjunct of Subread v1.6.
FeatureCounts of Subread package was adopted for counting reads to genomic features such as genes, exons, promoters, and genomic bins.The differential expression analysis between EH and EL was performed by using edgeR package.
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: A csv file include the normalized expression values of all genes for each Sample
|
| |
|
| Submission date |
Nov 27, 2018 |
| Last update date |
May 31, 2019 |
| Contact name |
Xiang Ma |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing Agriculture University
|
| Street address |
Weigang No.1
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL11429 |
| Series (1) |
| GSE122983 |
Transcriptome Analysis of the Endometrium from Chinese Erhualian sows that differ in Calcium Ion Concentration and Litter Size |
|
| Relations |
| BioSample |
SAMN10485172 |
| SRA |
SRX5065619 |
