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Status |
Public on Apr 17, 2020 |
Title |
G1E-ER4_Bcl11a+55KO_input |
Sample type |
SRA |
|
|
Source name |
G1E-ER4_Bcl11a+55KO_input
|
Organism |
Mus musculus |
Characteristics |
cell line: G1E-ER4 cell type: Erythroid cells differentiation: Induced with 10 nM estradiol for 24 hours
|
Treatment protocol |
The ATF4 binding motif at the Bcl11a +55 enhancer was disrupted using a CRISPR-Cas9-mediated approach in pooled G1E-ER4 cells.
|
Growth protocol |
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. Libraries were prepared using TruSeq ChIP-seq Sample Preparation Kit (Part# IP-202-1012) according to Illumina's instructions.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
2227_Read1
|
Data processing |
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks
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|
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Submission date |
Jan 20, 2020 |
Last update date |
Apr 17, 2020 |
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 |
GPL19057 |
Series (2) |
GSE143961 |
HRI activates ATF4 to promote BCL11A transcription and fetal hemoglobin silencing [ChIP-seq] |
GSE143963 |
HRI activates ATF4 to promote BCL11A transcription and fetal hemoglobin silencing |
|
Relations |
BioSample |
SAMN13893256 |
SRA |
SRX7584822 |