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| Status |
Public on May 25, 2022 |
| Title |
Adult erythroblasts rep2 |
| Sample type |
SRA |
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| Source name |
Adult erythroblasts
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| Organism |
Homo sapiens |
| Characteristics |
tissue/cell type: CD34+ cells derived from adult peripheral blood
cell type: Erythroid cells
differentiation: Differentiated day11
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| 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 For phase 2 medium, the interleukin-3 was withdrawn after 9 days of culture.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.
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| 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| 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
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| Submission date |
Aug 21, 2021 |
| Last update date |
May 27, 2022 |
| Contact name |
Peng Huang |
| E-mail(s) |
waliays@gmail.com
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| Organization name |
Guangzhou Medical University
|
| Department |
GMU-GIBH Joint School of Life Sciences
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| Lab |
Peng Huang
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| Street address |
Xinzao, Panyu District
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
511436 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN20923619 |
| SRA |
SRX11857127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5530944_3396_hg38.bigwig |
303.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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