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Sample GSM2794017 Query DataSets for GSM2794017
Status Public on Jul 15, 2018
Title WGBS from Gatad2a-/- system, Day4
Sample type SRA
 
Source name Gatad2a-/- cell line, Day4 post DOX induction
Organism Mus musculus
Characteristics tissue: Gatad2a-/- cell line
genotype: Gatad2a-/-
stage of reprogramming: Day4
Treatment protocol Reprogramming dynamics samples were generated by adding Dox to Secondary MEF. iPSC samples were harvested after 3-4 days of growth in N2B27 2i\LIF medium. Reprogramming samples of days 3-8, and iPSC samples were plated on irradiated human foreskin fibroblasts (HFF).
Growth protocol Maintenance and reprogramming (Day 3 and beyond) of murine naïve pluripotent cells were conducted in bovine serum-free N2B27-based media or KSR media: N2B27- based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen; 17502048), 5ml B27 supplement (Invitrogen; 17504044), 15% knockout serum replacement (Invitrogen – 10828), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 5mg/ml BSA (Sigma). KSR media: 500 ml DMEM (Invitrogen), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin- streptomycin (Invitrogen). Naïve conditions for murine PSCs included 10μg recombinant human LIF (Millipore; LIF1005). Where indicated 2i was added 48 hours after OSKM induction: small-molecule inhibitors CHIR99021 (CH, 3μM- Axon Medchem) and PD0325901 (PD 0.2 or 1μM - Axon Medchem).
Extracted molecule genomic DNA
Extraction protocol Cells were harvested at different time points according to the protocol. DNA was then isolated from cells using the Quick-gDNA mini prep kit (Zymo), followed by bisulfite convertion using the EZ DNA Methylation-Gold kit (Zymo).
Sequencing libraries were created using the EpiGnome Methyl-Seq (Epicentre) .
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
 
Data processing We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were aligned to mm10 reference genome using proprietary software, which is based on bowtie2, and is available for download here: https://tanaylab.bitbucket.io/misha/. In cases where the two reads were not aligned in a concordant manner, the reads were discarded.
for each CpG site, the numbers of methylated and unmethylated reads were counted.
Genome_build: mm10
Supplementary_files_format_and_content: The tab file is the output of misha software. Each file consists of chromosomal location (like a bed file), the number of methylated reads and number of unmethylated reads in each location.
 
Submission date Sep 26, 2017
Last update date May 15, 2019
Contact name Noa Novershtern
E-mail(s) noa.novershtern@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Molecular Genetics
Street address Weizmann Institute
City Rehovot
ZIP/Postal code 7610001
Country Israel
 
Platform ID GPL19057
Series (2)
GSE102518 High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems
GSE104283 High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [WGBS]
Relations
BioSample SAMN07702792
SRA SRX3217273

Supplementary file Size Download File type/resource
GSM2794017_WGBS_D4_P66KO.tab.gz 102.1 Mb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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