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Sample GSM5271206 Query DataSets for GSM5271206
Status Public on May 25, 2022
Title ChIP-Seq HUDEP2 cells WT GATA1 ChIP-seq rep2
Sample type SRA
Source name HUDEP2 cells
Organism Homo sapiens
Characteristics tissue: Immortalized Human Erythroid Progenitor
cell type: Erythroid cells
differentiation: Undifferentiated
genotype: WT
chip antibody: GATA1 (Abcam, Ab11852, lot GR3280668)
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.
G1E-ER4 cells were cultured with IMDM supplemented with 15% FBS, 2% penicillin/streptomycin, 0.6% Kit ligand conditioned medium, 0.15 mM monothioglycerol and 2 units/ml erythropoietin
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Samples were processed for library construction for Illumina sequencing using Illumina’s TruSeq ChIP Sample Preparation Kit (Illumina cat# IP-202-1012) according to Illumina's instructions..
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
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
Reads were mapped to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800. Peaks were called using MACS2. Peaks overlapped with blacklist were further filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks
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)
GSE173584 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (ChIP-Seq)
GSE173587 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development
BioSample SAMN18925781
SRA SRX10714820

Supplementary file Size Download File type/resource
GSM5271206_3134_hg38.bigwig 297.1 Mb (ftp)(http) BIGWIG
GSM5271206_3134_peaks_clean.bed.gz 1.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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