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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 05, 2022 |
| Title |
TKO,DMSO,BS,rep1 |
| Sample type |
SRA |
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| Source name |
TKO
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| Organism |
Mus musculus |
| Characteristics |
cell line: TKO
cell type: iMEFs
genotype: TKO
treatment: DMSO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
500 ng of genomic DNA was sheared by sonication to 100-500 bp using a Covaris S220 and purified by AMPure XP beads (Agencourt Bioscience Corp.). Genomic DNA libraries were constructed as ChIP-seq library. After adapter ligation, the DNA was treated with sodium bisulfite using EZ DNA Methylation GOLD kit (ZYMO RESEARCH) following the manufacturer’s instructions. Enrichment for adapter-ligated DNA was carried out through 10 PCR cycles using Pfu Turbo Cx Hotstart DNA polymerase (Agilent).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
The trimmed reads were mapped to the mouse GRCm38 genome assembly using Bismark v0.14.1 with single-end and non-directional mapping parameters
The methylation level of each CpG site was calculated as follows: number of methylated reads/number of total reads.
Assembly: mm10
Supplementary files format and content: txt
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| Submission date |
Apr 02, 2022 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Kei Fukuda |
| E-mail(s) |
kefukuda8@gmail.com
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| Organization name |
RIKEN
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| Lab |
Cellular memory
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| Street address |
2-1 Hrosawa, Wakoshi
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| City |
Saitama |
| State/province |
Japan |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE200010 |
Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [MethylC-seq] |
| GSE200016 |
Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway |
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| Relations |
| BioSample |
SAMN27252637 |
| SRA |
SRX14708485 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6001980_BS-TKO-rep1.bam.meth.txt.gz |
79.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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