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| Status |
Public on May 25, 2022 |
| Title |
ciTotiSC RRBS-seq rep1 |
| Sample type |
SRA |
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| Source name |
ciTotiSC induced from OG2 mESC
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| Organism |
Mus musculus |
| Characteristics |
cell line: OG2
cell type: ciTotiSC
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| Growth protocol |
ciTotiSCs were cultured in KSR basal medium composed of KO DMEM, 5% KSR (Gibco, 10828010), CDL (CD lipid concentrate, 500X, Gibco, 11905-031), 1% N2 (ThermoFisher, A1370701), 1X L-glutaMAX, 1X penicillin-streptomycin, 1X non-essential amino acids (NEAA), 1X sodium pyruvate, 55 μM 2-mercaptoethanol and 1000 U/mL mouse leukemia inhibitory factor (mLIF), 50 ng/ml Sodium L-ascorbyl-2-phosphate (Selleck, S5115) supplemented with 2.5 μM 1-Azakenpaullone (Selleck, S7193), 0.5 μM WS6 (Selleck, S7442) and 0.2 μM TTNPB (Selleck, S4627). Cells were passaged every 2-3 days using 0.05% Trypsin-EDTA at a ratio of 1:3-1:5 on inactivated MEF feeder layers.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs were extracted using DNeasy Blood and Tissue Kits (QIAGEN) and digested by MspI (NEB).
The digested DNAs were filled in and tailed. Then, bisulfate conversion was performed using MethyCode bisulfite conversion kit (Invitrogen). After amplification and purification，all libraries were constructed and subjected to 150 bp paired-ends Illumina Novaseq 6000 platform.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads were trimmed adaptors, and were mapped to the reference genome mm10 using BS-Seeker2 (v2.1.1) (parameter: -m 0.06) in mode of bowtie
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for ciTotiSC RRBS-seq rep1
Supplementary_files_format_and_content: bigwig file for ciTotiSC RRBS-seq rep1
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| Submission date |
Sep 29, 2021 |
| Last update date |
Jun 27, 2022 |
| Contact name |
Pengcheng Tan |
| E-mail(s) |
tpchengbjhd@126.com
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| Organization name |
Tsinghua University
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| Street address |
30 Shuangqing Rd
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| City |
Haidian |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE185004 |
Induction of mouse totipotent stem cells by a defined chemical cocktail [RRBS] |
| GSE185005 |
Induction of mouse totipotent stem cells by a defined chemical cocktail |
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| Relations |
| BioSample |
SAMN21899211 |
| SRA |
SRX12403369 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5603059_RRBS1.bw |
8.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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