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Sample GSM5530943 Query DataSets for GSM5530943
Status Public on May 25, 2022
Title Adult erythroblasts rep1
Sample type SRA
 
Source name Adult erythroblasts
Organism Homo sapiens
Characteristics tissue/cell type: CD34+ cells derived from adult peripheral blood
cell type: Erythroid cells
differentiation: Differentiated day11
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. Human CD34+ HSPCs were cultured using a three-phase protocol. For phase 1 medium, IMDM was supplemented with 100 ng/mL of human stem cell factor, 1 ng/mL of interleukin-3, 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 200 μg/mL of holotransferrin, 10 μg/mL of insulin, 5% human male A/B plasma, and 10 mg/mL of heparin. For phase 2 medium, the interleukin-3 was withdrawn after 9 days of culture. For phase 3, the cells were cultured with IMDM supplemented with 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 1 mg/mL of holotransferrin, 10 μg/mL of insulin, 5% human A/B plasma, and 10 μg/mL of heparin.
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 Aug 21, 2021
Last update date May 27, 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)
GSE173582 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (ATAC-Seq)
GSE173587 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development
Relations
BioSample SAMN20923618
SRA SRX11857126

Supplementary file Size Download File type/resource
GSM5530943_3395_hg38.bigwig 315.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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