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| Status |
Public on May 13, 2021 |
| Title |
DNMT3A1-W330R_RRBS_parental |
| Sample type |
SRA |
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| Source name |
C3H10T1/2 cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: C3H10T1/2
cell type: C3H embryo-derived mesenchymal progenitor cells
genotype: Parental line expressing FLAG-HA tagged W330R DNMT3A1
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| Growth protocol |
C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from flash frozen cell pelets of about 2 million cells using DNeasy Blood & Tissue Kit (Qiagen, 69509)
100 ng of genomic DNA were digested with 100U of MspI (NEB) and end-repaired/A-tailed using Kapa Hyper Prep kit (Kapa Biosystems). After ligation of Illumina-sequencing compatible indexes, DNA was purified using a 1X Agencourt AMPure XP bead clean up (Beckman Coulter). Bisulfite conversion was carried out using the Zymo EZ DNA kit (Zymo Research) using the following program: 55 cycles: 95°C 30s, 50°C 15 min, 4°C hold. Libraries were amplified 17 cycles using Uracil+ Ready mix (Kapa Biosystems, KK2801). The resulting libraries, mean size 388bp, were normalized to 3nM, pooled and clustered on a pair end read flow cell and sequenced for 100 cycles on a NovaSeq6000 (Illumina).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For ChIP-seq DNA input: Following alignment with BWA, bigwigs were generated with read coverage for 200-bp bins smoothed across 1-kb, computed with deepTools bamCoverage. Excludes mm10 ENCODE blacklist regions.
For ChIP-seq signal: Following alignment with BWA, bigwigs were generated with enrichment scores represented as input-normalized (log2-ratio), read-depth normalized signal per 200-bp bins, smoothed across 1-kb bins using deepTools. Excludes mm10 ENCODE blacklist regions. See publication Methods for details.
For ChIP-seq signal peaks: Following alignment with BWA, SICER2 was used to call broad H2AK119Ub peaks. Processed output is a BED file in the format "chrom, start, end, read-count".
For RRBS: Following alignment with Bismark, bedGraph files were generated representing methylation scores at CpGs of at least 10X read coverage, computed using MethylDackel. See publication Methods for details.
Genome_build: mm10 for Mus musculus, dm6 for Drosophila melanogaster
Supplementary_files_format_and_content: Filetype suffix explanation: bw = bigWig
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| Submission date |
Feb 01, 2021 |
| Last update date |
May 14, 2021 |
| Contact name |
Jacek Majewski |
| Organization name |
McGill University
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| Department |
Human Genetics
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| Street address |
740 Dr Penfield Ave
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3A 0G1 |
| Country |
Canada |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE147879 |
Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at CpG islands |
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| Relations |
| BioSample |
SAMN17732575 |
| SRA |
SRX10000625 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5058943_DNMT3A1-W330R_RRBS_parental.bedGraph.gz |
14.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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