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Sample GSM2371313 Query DataSets for GSM2371313
Status Public on Jan 01, 2018
Title ATAC-seq_5F_D4-shEZH1-rep1
Sample type SRA
 
Source name Human MSCiPS1-derived 5F hematopoietic cells
Organism Homo sapiens
Characteristics tissue: Hematopoietic cells
Treatment protocol NA
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) and puromycin was added at 0.35 ug/mL (ThermoFisher). Cultures were maintained at a density of <1 x106 cells/ml, and media were changed every 3-4 days. AGM tissue was microdissected from E10.5 embryos and dissociated to single cells. AGM hematopoietic cells were sorted for immunophenotypic markers cKit+VE-cadherin+CD45+CD41+.
Extracted molecule genomic DNA
Extraction protocol For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human (hg19) or mouse (mm9) genome were retained for downstream data analysis.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) or mouse genome assembly mm9 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 (http://liulab.dfci.harvard.edu/MACS/).
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, mm9
Supplementary_files_format_and_content: wig file and peak bed file
 
Submission date Nov 02, 2016
Last update date May 15, 2019
Contact name Melissa Kinney
E-mail(s) melissa.kinney@childrens.harvard.edu
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)
GSE89416 ATAC-seq analysis in 5F cells and AGM cells with EZH1 depletion
GSE89418 EZH1 as a key epigenetic barrier to definitive haematopoiesis during embryonic development
Relations
BioSample SAMN05967260
SRA SRX2319389

Supplementary file Size Download File type/resource
GSM2371313_ATAC-seq_5F_D4-shEZH1-rep1.wig.gz 248.3 Mb (ftp)(http) WIG
GSM2371313_ATAC-seq_5F_D4-shEZH1-rep1_peaks.bed.gz 928.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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