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Sample GSM5271198 Query DataSets for GSM5271198
Status Public on May 25, 2022
Title Capture-C HUDEP2 cells WT rep3
Sample type SRA
 
Source name HUDEP2 cells
Organism Homo sapiens
Characteristics tissue: Immortalized Human Erythroid Progenitor
cell type: Erythroid cells
differentiation: Differentiated for 5 days
genotype: WT
Treatment protocol HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.
Growth protocol 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 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).
Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Description BCL_3096_3099_WT_nor.bigwig
HS3_3096_3099_WT_nor.bigwig
Data processing Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with the normalized Capture-C interaction signals
 
Submission date Apr 29, 2021
Last update date May 25, 2022
Contact name Peng Huang
E-mail(s) waliays@gmail.com
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)
GSE173583 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (Capture-C)
GSE173587 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development
Relations
BioSample SAMN18925793
SRA SRX10714812

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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