|
| Status |
Public on Jul 24, 2021 |
| Title |
TKOL_P10 |
| Sample type |
SRA |
| |
|
| Source name |
J1 mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
strain: J1
genotype: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA
|
| Treatment protocol |
N/A
|
| 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 |
Purelink Genomic DNA mini kit (Invitrogen)
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WGBS
|
| Data processing |
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Genome_build: mm9
processed data files format and content: bigWig file of 10X 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 |
GPL24247 |
| Series (1) |
| GSE158460 |
Dnmt1 has global de novo methylation activity and is specifically targeted to transposable elements |
|
| Relations |
| BioSample |
SAMN20360226 |
| SRA |
SRX11531297 |
