|
| Status |
Public on Mar 03, 2023 |
| Title |
Control CN2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Sus scrofa |
| Characteristics |
strain: Landrace x Yorkshire x Duroc (LYD)
tissue: whole embryo
age: embryonic day 21
treatment: untreated
|
| Treatment protocol |
In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.
|
| Growth protocol |
After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two LYD surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole CN embryos (n = 3) and whole PA embryos (n = 3) samples was isolated with TRIzol reagent. DNase I was treated to the RNA samples to avoid genomic DNA contamination. One ug of total RNA was used to construct cDNA libraries with the TruSeq RNA Sample Prep Kit v.2.
RNA libraries were prepared for sequencing according to Illumina's instructions accompanying the TruSeq RNA Sample Prep Kit v.2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
Then, the cleaned reads were aligned to the reference genome (Sscrofa11.1) using STAR (v2.7.5) with default parameters.
Duplicated reads were removed using Picard MarkDuplicates and reads were filtered using SAMtools (-q 30).
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text files containing normalized read counts from Salmon (v1.3.0)
|
| |
|
| Submission date |
Nov 21, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Jinsoo Ahn |
| E-mail(s) |
ahn.134@osu.edu
|
| Organization name |
The Ohio State University
|
| Street address |
2029 Fyffe Rd
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL19176 |
| Series (2) |
| GSE218485 |
RNA-seq of porcine parthenogenetic embryos |
| GSE218487 |
RNA-seq and WGBS of parthenogenetic pig embryos |
|
| Relations |
| BioSample |
SAMN31820870 |
| SRA |
SRX18333074 |
