|
| Status |
Public on Apr 17, 2020 |
| Title |
G1E-ER4_Bcl11a+55KO_ATF4-r1 |
| Sample type |
SRA |
| |
|
| Source name |
G1E-ER4_Bcl11a+55KO_ATF4
|
| Organism |
Mus musculus |
| Characteristics |
cell line: G1E-ER4
cell type: Erythroid cells
differentiation: Induced with 10 nM estradiol for 24 hours
chip antibody: ATF4 (Cell Signaling Technology, 11815S, lot 4)
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2228_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
|
| |
|
| Submission date |
Jan 20, 2020 |
| Last update date |
Apr 18, 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 |
SAMN13893255 |
| SRA |
SRX7584823 |
