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Sample GSM7108084 Query DataSets for GSM7108084
Status Public on Jul 01, 2024
Title U2OS-KRAB-IDR3-TCF3, H3K9me3, ABCAM, input, rep2
Sample type SRA
 
Source name U2OS
Organism Homo sapiens
Characteristics cell line: U2OS
cell type: Human Bone Osteosarcoma Epihelial Cells
chip antibody: none
Growth protocol DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells were washed in FBS-free media then cross-linked with 1% formaldehyde for 10 min at room temperature, Cross-linked cells were washed with ice-cold PBS, For each sample, 20 million fixed cells were lysed to prepare nuclear extracts.
For ChIP-Seq, 5ng of purified ChIP DNA were used to generate the sequencing library using a NEB kit and sequenced with the Illumina HiSeq X Ten.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description IP_1_peaks.broadPeak
Data processing Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Trimgalore v0.6.7, discarding reads left with < 30 bp
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie2 version 2.5.0. Only uniquely mapping reads with were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.01
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
 
Submission date Mar 20, 2023
Last update date Jul 01, 2024
Contact name YING FENG
E-mail(s) fengying@mail.ecust.edu.cn
Organization name Shanghaitech University
Street address 393 Middle Huaxia Road
City Shanghai
ZIP/Postal code 201210
Country China
 
Platform ID GPL24676
Series (1)
GSE227780 The Local Density of H3K9me3 Dictates The Stability of HP1a Condensates-mediated Genomic Interactions
Relations
BioSample SAMN33833092
SRA SRX19734331

Supplementary file Size Download File type/resource
GSM7108084_R22037391_INPUT_2_KRAB_IDR3_TCF3_R1_unique.bw 138.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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