|
| Status |
Public on May 25, 2022 |
| Title |
ChIP-Seq HUDEP2 cells HIC2-ER induced HA ChIP-seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HUDEP2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Immortalized Human Erythroid Progenitor
cell type: Erythroid cells
differentiation: Undifferentiated
genotype: HIC2-ER OE
chip antibody: HA (Bethyl Laboratories, A190-108A, lot 10)
treatment: Induced with 10 nM tamoxifen for 24hrs
|
| 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.
G1E-ER4 cells were cultured with IMDM supplemented with 15% FBS, 2% penicillin/streptomycin, 0.6% Kit ligand conditioned medium, 0.15 mM monothioglycerol and 2 units/ml erythropoietin
|
| 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). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Samples were processed for library construction for Illumina sequencing using Illumina’s TruSeq ChIP Sample Preparation Kit (Illumina cat# IP-202-1012) according to Illumina's instructions..
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| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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
Reads were mapped to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800. Peaks were called using MACS2. Peaks overlapped with blacklist were further filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks
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| |
|
| 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) |
| GSE173584 |
HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (ChIP-Seq) |
| GSE173587 |
HIC2 represses BCL11A transcription to regulate hemoglobin switching during development |
|
| Relations |
| BioSample |
SAMN18925816 |
| SRA |
SRX10714831 |
