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Sample GSM5271191 Query DataSets for GSM5271191
Status Public on May 25, 2022
Title ATAC-Seq HUDEP2 cells HIC2 OE rep2
Sample type SRA
Source name HUDEP2 cells
Organism Homo sapiens
Characteristics tissue: Immortalized Human Erythroid Progenitor
cell type: Erythroid cells
differentiation: Undifferentiated
genotype: HIC2 OE
Growth protocol HUDEP1 and HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.
Extracted molecule genomic DNA
Extraction protocol 50-100k cells were lysised with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin, then incubated with Tagment DNA Enzyme (Illumina) for 30 minutes at 37C. DNA was purified with Qiagen MinElute Reaction Cleanup Kit.
Library fragments were amplified using Phusion High-Fidelity PCR Master Mix with HF Buffer (ThermoFisher cat#F531S) and custom v2_Ad1 and v2_Ad2 unique dual indexes (Mezger, et al., 2018, Nat Commun).
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 2000
Data processing Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Mapping to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files with read coverage
Submission date Apr 29, 2021
Last update date May 27, 2022
Contact name Peng Huang
Organization name Guangzhou Medical University
Department GMU-GIBH Joint School of Life Sciences
Lab Peng Huang
Street address Xinzao, Panyu District
City Guangzhou
State/province Guangdong
ZIP/Postal code 511436
Country China
Platform ID GPL30173
Series (2)
GSE173582 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (ATAC-Seq)
GSE173587 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development
BioSample SAMN18925803
SRA SRX10714805

Supplementary file Size Download File type/resource
GSM5271191_3088_hg38.bigwig 353.6 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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