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| Status |
Public on Oct 28, 2020 |
| Title |
mESC_CUTTag_H3K27me3_2000_rep2 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cell
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| Organism |
Mus musculus |
| Characteristics |
tissue: Embryonic stem cell
genotype: wild-type
developmental stage: Embryonic stem cell
antibody: H3K27me3 (CST 9733s)
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| Growth protocol |
Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-025-CIR).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The CUT&Tag is performed according to previously described (cite CT paper) with CUT&Tag kit (Vazyme Biotech, TD091). Briefly, cells were incubated with 10μl pre-washed ConA beads (Vazyme Biotech, TD091) in 1.5ml low-binding tube. 50μl antibody buffer (Vazyme Biotech, TD091) with 0.5μg antibody was added and cultured for 2 hours at room temperature. After twice of wash with dig-wash buffer (Vazyme Biotech, TD091), 50μl dig-wash buffer with 0.5μg secondary antibody was added and incubated at room temperature for 30min. After twice of wash with 800μl dig-wash buffer, 0.58μl pG-Tn5 was added with 100μl dig-300 buffer (Vazyme Biotech, TD091). Samples were incubated at room temperature for 1 hours and then washed twice with 800μl dig-300 buffer. 300μl tagmentation buffer was added and samples were incubated at 37°C for 1 hours. The reaction was stopped with 10μl 0.5M EDTA，3 μl 10% SDS和2.5μl 20 mg/ml Proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries (Vazyme Biotech, TD091).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Library strategy: CUT&Tag
Basecalls performed using CASAVA version 1.8
CUT&Tag reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 109bp bin in the genome
Genome_build: mm9
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| Submission date |
Apr 14, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
Bofeng Liu |
| E-mail(s) |
lbf12thu@gmail.com
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| Organization name |
Tsinghua University
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| Department |
School of Life Science
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| Lab |
Xie Wei Lab
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| Street address |
Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE135457 |
The landscape of RNA Pol II binding reveals a step-wise transition during ZGA |
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| Relations |
| BioSample |
SAMN14598124 |
| SRA |
SRX8115729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4476406_mESC_CUTTag_H3K27me3_2000_rep2.bedGraph.gz |
25.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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