|
| Status |
Public on Aug 21, 2020 |
| Title |
Parthenote PA1 [BiSulfite-seq] |
| 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: parthenogenesis
|
| 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, 200 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 |
genomic DNA |
| Extraction protocol |
From the whole collected embryos of CN and PA (n = 3 for each), genomic DNA was isolated and fragmented.
For optimization of bisulfite conversion of genomic DNA, Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Inc. Ann Arbor, MI, USA) was used according to the manufacturer`s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
The cleaned reads were aligned to the reference genome (Sscrofa11.1) using BSMAP (v2.87) with default parameter settings.
Using methylatio.py script in BSMAP, extraction of the methylation ratio of every single cytosine from the mapping results was conducted.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files include methylation ratios for each sample.
Supplementary_files_format_and_content: Bigwig files contain data that will be diplayed in genome browsers.
|
| |
|
| Submission date |
Aug 18, 2020 |
| Last update date |
Aug 21, 2020 |
| 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 |
GPL22918 |
| Series (1) |
| GSE156439 |
Whole genome bisulfite sequencing (WGBS) of porcine parthenogenetic embryos and wild-type controls. |
|
| Relations |
| BioSample |
SAMN15850710 |
| SRA |
SRX8965691 |
