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Sample GSM4459843 Query DataSets for GSM4459843
Status Public on May 13, 2020
Title MT-TY1-HRP2-W21A-input
Sample type SRA
 
Source name muscle
Organism Mus musculus
Characteristics cell line: C2C12
tissue: muscle
cell type: myotube
chip antibody: none
Growth protocol C2C12 cells were cultured in DMEM medium supplemented with 20% fetal bovine serum (FBS).
Extracted molecule genomic DNA
Extraction protocol For TY1,HRP2 and DPF3a ChIP, cells were double cross-linked with DMA and 1% formaldehyde. For H3K36me2 ChIP, cells were cross-linked with 1% formaldehyde. The crosslink was stopped by adding 2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed withTY1, HRP2 (15134-1-AP), DPF3a and H3K36me2 (ab9049). After elution and reversal cross-linking, DNA was purified and sequenced on HiSeq X ten.
Construction of ChIP-seq library was performed using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing ChIP-seq data were processed according to ENCODE Processing Pipeline.
Clean reads were mapped to Mus musculus genome (mm10) by BWA (version 0.7.13)
Peaks were called using peak finding algorithm MACS2 (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated by deeptools
 
Submission date Apr 08, 2020
Last update date May 14, 2020
Contact name Bingxue Lan
Organization name Tianjin Medical University
Street address Qixiangtai road
City Tianjin
ZIP/Postal code 300070
Country China
 
Platform ID GPL21273
Series (2)
GSE141407 HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription
GSE148295 HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription [ChIP-Seq]
Relations
BioSample SAMN14558851
SRA SRX8082206

Supplementary file Size Download File type/resource
GSM4459843_MT-TY1-HRP2-W21A-input.bw 227.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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