|
| Status |
Public on Nov 25, 2019 |
| Title |
SO2 |
| Sample type |
SRA |
| |
|
| Source name |
Oocyte
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Prepubertal gilts
size: Small (1.5-1.9 mm)
|
| Treatment protocol |
Porcine ovaries were collected from prepubertal gilts at a local abattoir and transported to our laboratory in flask within 3 h after slaughter. Ovaries were washed three times with saline solution. COCs were aspirated from small follicles with diameter 1.5-1.9 mm (SO) using a 23-gauge needle attached to a 5 mL syringe or from large follicles with diameter from 3 to 6 mm (LO) using 20-gauge needle attached to a 10 mL syringe.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from denuded oocytes of the two different groups (three replicates each, n= 360) using an AllPrep DNA/RNA Micro Kit (Qiagen) according to the manufacturer’s instructions.
The RNA libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
After importing of FASTQ files, raw sequencing reads were trimmed based on quality score (Q-score >20 was considered high-quality data), removal of adaptor sequences and discarding reads with length <15 bp.
Sequence reads were mapped and annotated to the Sus scrofa reference genome with genes and transcripts
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization)
Expression analysis has been done using Differential Expression In Two Groups tool of CLC Genomics Workbench v. 12.0 based on a negative binomial Generalized Linear Model (GLM) function.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: A matrix table including total read count and Tags Per Million (TPM) values for each sample with gene ID.
|
| |
|
| Submission date |
Apr 17, 2019 |
| Last update date |
Nov 25, 2019 |
| Contact name |
Ahmed Gad |
| E-mail(s) |
ahmed.y.gad@agr.cu.edu.eg
|
| Organization name |
Colorado State University
|
| Department |
Biomedical Sciences
|
| Lab |
ARBL
|
| Street address |
3107 Rampart Rd
|
| City |
Fort Collins |
| State/province |
Colorado |
| ZIP/Postal code |
80521 |
| Country |
USA |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE129994 |
Transcriptome profiles of porcine oocytes with different developmental competence |
|
| Relations |
| BioSample |
SAMN11457930 |
| SRA |
SRX5706614 |
