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Sample GSM4142028 Query DataSets for GSM4142028
Status Public on May 11, 2020
Title H3K27ac_HiChIP_MED14-dTAG_2h_DMSO_B
Sample type SRA
 
Source name H3K27ac_HiChIP_MED14-dTAG_2h_DMSO
Organism Homo sapiens
Characteristics cell line: KBM7
cell type: chronic myeloid leukemia cell line
genotype/variation: MED14-dTAG
treatment: 2h DMSO
chip antibody: H3K27ac (Abcam ab4729)
Treatment protocol 15mio cells were treated for 2h with 500nM dTAG7 or DMSO and then fixed with 1% MeOH-free PFA for 10min at room temperature.
Growth protocol KBM7 cells were grown in IMDM medium supplemented with 10% FBS and 1% Pen/Strep.
Extracted molecule genomic DNA
Extraction protocol Chromatin contacts were generated and pulldown performed as previously described (PMID: 27643841).
Library construction using Illumina Tn5.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Data processing conversion and demultiplexing: Illumina2bam
FASTQ files were in silico digested by looking for the restriction enzyme religations sites GATCGATC. Only the 5 prime part of a read is kept after removing the remainder of a read when cut at the restriction site. All non cut reads are kept.
All filtered reads are then mapped to human genome assembly hg19 with bowtie2 (version 2.2.3) using options --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
The human genome was insilico digested with MboI enzyme and mapped reads are assigned to the insilico digested genome fragments. Read pairs are tagged as valid if they had the correct orientation and are on different fragments.
Genome_build: hg19
Supplementary_files_format_and_content: hic generation: .hic files were generated with the 'pre' tool from juicer tools (version 1.8.9).
 
Submission date Oct 28, 2019
Last update date May 12, 2020
Contact name Georg E Winter
Organization name CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14, AKH BT25.3
City Wien
State/province Austria
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL21290
Series (2)
GSE139466 Selective Mediator-dependence of cell type-specifying transcription [HiChIP]
GSE139468 Selective Mediator dependence of cell-type-specifying transcription
Relations
BioSample SAMN13139826
SRA SRX7064289

Supplementary file Size Download File type/resource
GSM4142028_H3K27ac_HiChIP_MED14-dTAG_2h_DMSO_B.hic 222.7 Mb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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