|
| Status |
Public on Jul 24, 2021 |
| Title |
DKO0_Nanopore |
| Sample type |
SRA |
| |
|
| Source name |
J1 mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
strain: J1
genotype: Dnmt3a + Dnmt3b KO
|
| Treatment protocol |
Passaged fifteen times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid
|
| Growth protocol |
mES cells were cultured in Knock Out DMEM media (Gibco) containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. For ES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CD1 mouse embryonic fibroblasts (MEFs) were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells per well of a six-well plate and were split every 3–4 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from 16 million cells through phenol-chloroform extraction
Ligation Sequencing Kit SQK-LSK109 (manufacturer's recommendation)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Description |
Nanopore sequencing
|
| Data processing |
Library strategy: DNA-seq
Nanopore long reads data was processed using the Nanopype pipeline (v1.1.0). The basecaller Guppy (v4.0.11) was used with the r9.4.1 fast configuration. Quality filtering was disabled for any basecalling.
Genome wide methylation rates were obtained by aligning all reads against reference genome mm9 using NGMLR (v0.2.7) followed by nanopolish (v0.13.2) using default parameters and filtered for CpGs with 15x coverage.
Genome_build: mm9
processed data files format and content: bigWig file of coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)
|
| |
|
| Submission date |
Jul 23, 2021 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Helene Kretzmer |
| E-mail(s) |
kretzmer@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Genome Regulation
|
| Lab |
Meissner Lab
|
| Street address |
Ihnestraße 63
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26624 |
| Series (1) |
| GSE158460 |
Dnmt1 has global de novo methylation activity and is specifically targeted to transposable elements |
|
| Relations |
| BioSample |
SAMN20360233 |
| SRA |
SRX11531303 |
