|
| Status |
Public on Dec 25, 2019 |
| Title |
PGCs 15dpf rep2 |
| Sample type |
SRA |
| |
|
| Source name |
PGCs 15dpf
|
| Organism |
Oryzias latipes |
| Characteristics |
strain: Hd-rR
tissue: primordial germ cells
developmental stage: 15dpf
|
| Treatment protocol |
wildtype
|
| Growth protocol |
The medaka strain Hd-rR was used and maintained under standard conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA and total RNA from each embryo samples were extracted using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Cat No.: 80224) according to the manufacturer’s instruction.
Whole genome bisulfite sequencing (WGBS) libraries were prepared with NEBNext® Ultra™ II FS DNA Library Prep Kit (NEB, E7805S) according to the manufacturer’s user manual.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
P2
|
| Data processing |
Bismark (Version: v0.19.0) was used to map bisulfite sequencing reads onto medaka genome (Ensembl release-95) with default parameters (Krueger and Andrews, 2011). To guarantee getting the most accurate mapping result, we only retained the reads being mapped on unique position of genome. The utility “bismark_methylation_extractor” wrapped in Bismark was used to extract methylation levels on each site.
Genome_build: medaka genome (Ensembl release-95)
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Apr 17, 2019 |
| Last update date |
Dec 25, 2019 |
| Contact name |
Ramji Kumar Bhandari |
| E-mail(s) |
rkbhanda@uncg.edu
|
| Organization name |
University of North Carolina Greensboro
|
| Department |
Biology
|
| Lab |
Bhandari Laboratory
|
| Street address |
321 McIver St
|
| City |
Greensboro |
| State/province |
NC |
| ZIP/Postal code |
27412 |
| Country |
USA |
| |
|
| Platform ID |
GPL23039 |
| Series (1) |
| GSE130002 |
Bisulfite sequencing of medaka PGCs methylomes |
|
| Relations |
| BioSample |
SAMN11458123 |
| SRA |
SRX5706651 |
