 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 15, 2024 |
| Title |
PGCs, F04, R1 |
| Sample type |
SRA |
| |
|
| Source name |
PGCs, F04
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primordial germ cell
genotype: PCNA knockout
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
PGCs (GOF18-GFP+SSEA1+) were isolated from E12.5 embryos carrying the GOF18-GFP reporter by FACS into lysis buffer (Qiagen RLT plus buffer)
WGBS-sequencing libraries were prepared according to the bulk version of the published scBS-seq protocol (https://www.nature.com/articles/nprot.2016.187). Briefly, cells were lysed in RLT plus buffer (Qiagen) then bisulfite converted using the Zymo EZ-Direct kit. Converted DNA was prepared for Illumina sequencing via two rounds of random primed synthesis using oligos containing Illumina adapter sequences followed by PCR to amplify and incorporate indexes.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bismark v0.23.1 (https://doi.org/10.1093/bioinformatics/btr167) was used to align DNA reads to the bisulfite converted GRCm38 mouse genome then perform methylation calling.
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.
|
| |
|
| Submission date |
Jan 23, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Laura Biggins |
| E-mail(s) |
laura.biggins@babraham.ac.uk
|
| Organization name |
The Babraham Institute
|
| Department |
Bioinformatics
|
| Street address |
Babraham Research Campus
|
| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE253991 |
Primordial germ cell DNA demethylation and development require DNA translesion synthesis |
|
| Relations |
| BioSample |
SAMN39578744 |
| SRA |
SRX23367230 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8031552_lane7999_TGTGGTTG_F04_L001_R1_GRCm38_bismark_bt2.deduplicated.bismark.cov.gz |
248.5 Kb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
