|
| Status |
Public on Sep 02, 2020 |
| Title |
FH4 [RNA-Seq] |
| 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.
Each sample with RNA Integrity Number (RIN) value > 7.5 was used for following library preparation. Approximately 3μg RNA of each RNA-seq sample was used to remove ribosomal RNA (rRNA) using Epicentre Ribo-Zero™ rRNA removal Kit (Epicentre, USA). Each sample was amplified by PCR to enrich cDNA libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
FH4_FPKM
|
| Data processing |
Clean data from each library were obtained and then mapped to the reference genome (Sscrofa10.2) downloaded from the Ensembl Genomes (http://www.ensemblgenomes.org) using software Hisat2 (v2.0.1).
The mapped reads were assembled using StringTie V1.0.4 (Trapnell et al., 2012)
The assembled transcripts from each individual were merged with Cuffmerge to generate a single transcriptome annotation from Ensembl.
Rsem (V1.2.6) was used to calculate gene expression levels using the FPKM (Fragments per Kilo bases per Million reads) method for genes in each sample.
Differential expression analysis was performed by DESeq2 package (V1.6.3)
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 09, 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) |
| GSE134001 |
Transcriptome profiling of ovarian tissues from 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 |
SAMN12234787 |
| SRA |
SRX6419115 |
