|
| Status |
Public on May 25, 2022 |
| Title |
Capture-C HUDEP2 cells HIC2 OE rep2 |
| 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: HIC2 OE
|
| 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_3100_3103_HIC2_OE_nor.bigwig
HS3_3100_3103_HIC2_OE_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 |
SAMN18925788 |
| SRA |
SRX10714815 |
