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Sample GSM4801061 Query DataSets for GSM4801061
Status Public on Jun 18, 2021
Title DKO_0.35uM_1i_E35
Sample type SRA
 
Source name E3.5 Blastocyst
Organism Mus musculus
Characteristics cell type: E3.5 Blastocyst
strain: J1
genotype: Dnmt3a + Dnmt3b KO + Dnmt1 inhibitor
Treatment protocol Zygotes electroporated with Cas9-RNP with guides targeting Dnmt3a and Dnmt3b; 2C stage embryos were treated with 0.35uM Dnmt1i (GSK3484862) until blastocyst stage
Growth protocol Embryos were cultured in standard embryo media. In brief, 25uL of KSOM media drops were added to the petridish and covered with mineral oil. The culture dish with KSOm was pre-gassed prior to transfer of embryos.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from cells through phenol-chloroform extraction
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 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 GPL24247
Series (1)
GSE158460 Dnmt1 has global de novo methylation activity and is specifically targeted to transposable elements
Relations
BioSample SAMN16249153
SRA SRX9179173

Supplementary file Size Download File type/resource
GSM4801061_DKO_0.35uM_1i_E35.bw 188.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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