|
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)
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|
|
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>)
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|
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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 |