|
| Status |
Public on Sep 02, 2020 |
| Title |
FH4 |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Sus scrofa |
| Characteristics |
strain: Canadian Large White pig
tissue: ovary
age: on the 20 day (day 1 = first day of estrus) after estrus as in the follicular phase
genotype: high fecundity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated individually from the ovaries samples using TRIzol Reagent (Invitrogen), purified with RNeasy Mini Kit (Qiagen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bio-analyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel.
Illumina small RNA-Seq (RNA sequencing) libraries were constructed using NEBNext® Multiplex Small RNA library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The clean reads were obtained by masking adapters, poly-A tails and low-quality reads from the raw data with Trimmomatic10 (v0.30)
The clean reads were then aligned to the porcine genome sequence (Sscrofa10.2) by Bowtie2 (v2.1.0)
Unmapped reads were used to predict the novel miRNAs with miRDeep (v2.0.0.7)
Differentially expression analysis used the DEseq2 package, P-value < 0.05 and |log2 (fold change)| ≥ 1 were described as differentially expressed
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include miRNA expression information for each Sample
|
| |
|
| Submission date |
Jun 06, 2019 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Huiyan HU |
| E-mail(s) |
huhuiyan315@163.com
|
| Phone |
+86-312-7528343
|
| Organization name |
Hebei Agricultural University
|
| Street address |
Lekai South Street No. 2596
|
| City |
Baoding |
| ZIP/Postal code |
071000 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (2) |
| GSE132307 |
MicroRNA transcriptome profiling in ovarian tissues of pigs with extreme phenotypes for reproductive efficiency during the luteal and follicular phases of the estrous cycle |
| GSE134002 |
Profiling in ovarian tissues of pigs with extreme phenotypes for reproductive efficiency during the luteal and follicular phases of the estrous cycle |
|
| Relations |
| BioSample |
SAMN11969625 |
| SRA |
SRX5982431 |
