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Sample GSM4476409 Query DataSets for GSM4476409
Status Public on Oct 28, 2020
Title mESC_H3K4me3_CUTTag_200
Sample type SRA
 
Source name Embryonic stem cell
Organism Mus musculus
Characteristics tissue: Embryonic stem cell
genotype: wild-type
developmental stage: Embryonic stem cell
antibody: H3K4me3(Home-made)
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, 25-028-CIR).
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, TD094).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
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
 
Submission date Apr 14, 2020
Last update date Oct 29, 2020
Contact name Bofeng Liu
E-mail(s) lbf12thu@gmail.com
Organization name Tsinghua University
Department School of Life Science
Lab Xie Wei Lab
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (1)
GSE135457 The landscape of RNA Pol II binding reveals a step-wise transition during ZGA
Relations
BioSample SAMN14598121
SRA SRX8115732

Supplementary file Size Download File type/resource
GSM4476409_mESC_H3K4me3_CUTTag_2000.bedGraph.gz 8.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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