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Sample GSM2507992 Query DataSets for GSM2507992
Status Public on Jan 01, 2018
Title ChIP-seq_5F_shEZH1_H3K4me3_rep1
Sample type SRA
Source name Human MSCiPS1-derived 5F hematopoietic cells
Organism Homo sapiens
Characteristics tissue: Hematopoietic cells
Growth protocol MSCiPS1 human induced pluripotent stem cells were differentiated to CD34+ hematopoietic cells and transduced with 5 transcription factors (5F). Human 5F cells were cultured in SFEM with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3 (all R&D Systems). Dox was added at 2 μg/ml (Sigma). Puromycin was added at 0.35 ug/mL (ThermoFisher) and G418 was added at 750 ug/mL (Gibco). Media were changed every 3-4 days.
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description Streptavidin Dynabeads or Antibodies: Millipore 04-745, lot: 1997493
Data processing Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file, and peak bed file
Submission date Feb 24, 2017
Last update date May 15, 2019
Contact name Melissa Kinney
Organization name Boston Children's Hospital
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL18573
Series (2)
GSE89417 ChIP-seq analysis of EZH1, H3K4me3 and H3K27me3 in 5F cells
GSE89418 EZH1 as a key epigenetic barrier to definitive haematopoiesis during embryonic development
SRA SRX2588609
BioSample SAMN06465141

Supplementary file Size Download File type/resource
GSM2507992_ChIP-seq_5F_shEZH1_H3K4me3_rep1.wig.gz 77.5 Mb (ftp)(http) WIG
GSM2507992_ChIP-seq_5F_shEZH1_H3K4me3_rep1_peaks.bed.gz 271.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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