|
| Status |
Public on Jul 15, 2018 |
| Title |
WGBS from Mbd3f/- system, Day2 |
| Sample type |
SRA |
| |
|
| Source name |
Mbd3f/- cell line, Day2 post DOX induction
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mbd3f/- cell line
genotype: Mbd3f/-
stage of reprogramming: Day2
|
| 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 HiSeq 2500 |
| |
|
| 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 |
GPL17021 |
| 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 |
SAMN07702781 |
| SRA |
SRX3217263 |
