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Sample GSM4801051 Query DataSets for GSM4801051
Status Public on Jun 18, 2021
Title DKO0_Uhrf1_C5
Sample type SRA
 
Source name J1 mESC
Organism Mus musculus
Characteristics cell type: mESC
strain: J1
genotype: Dnmt3a + Dnmt3b + Uhrf1 KO
Treatment protocol CRISPR Cas9 mediated knockout of Uhrf1, passaged seven 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 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 HiSeq 4000
 
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 Sep 23, 2020
Last update date Jun 18, 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 GPL21103
Series (1)
GSE158460 Dnmt1 has global de novo methylation activity and is specifically targeted to transposable elements
Relations
BioSample SAMN16249164
SRA SRX9179163

Supplementary file Size Download File type/resource
GSM4801051_DKO0_Uhrf1_C5.bw 21.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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