|
| Status |
Public on May 25, 2022 |
| Title |
ATAC-Seq HUDEP1 cells HIC2 KO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HUDEP1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Immortalized Human Erythroid Progenitor
cell type: Erythroid cells
differentiation: Undifferentiated
genotype: HIC2 KO
|
| 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 |
| 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 |
SAMN18925798 |
| SRA |
SRX10714808 |
