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| Status |
Public on Jan 01, 2023 |
| Title |
G1ER_CHD7-KO_GATA2 |
| Sample type |
SRA |
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| Source name |
G1ER cell line
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| Organism |
Mus musculus |
| Characteristics |
cell line: G1ER
cell type: erythroblasts
genotype: Chd7-/-
antibody: GATA2 (Santa Cruz, sc9008)
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| Growth protocol |
Wild type and CHD7 knockout G1ER cells were grown and maintained in IMDM media containing heat-inactivated FBS (16%), pen/strep (2%), monothioglycerol (6.2 mL per 500 mL), EPO (2U/mL) and SCF conditioned media (0.6%). Cells were differentiated with beta-estradiol (10-7M final concentration). After 48 hrs of beta-estradiol treatment, differentiation was assessed using benzidine staining method (using o-diansidine from Sigma, D9143, ref – Orkin SH, Harosi FI, Leder P. PNAS 72 (1): 98-102, 1975).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with relevant antibody
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequences were aligned to UCSC build version GRCm38 version of mouse genome using Bowtie2 (version 2.2.1) (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20.
MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm was used to identify regions of ChIP-Seq peaks, with a q-value threshold of enrichment of 0.05 for all datasets.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: NarrowPeak bed files of binding peaks.
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| Submission date |
Jul 07, 2016 |
| Last update date |
Jan 01, 2023 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
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| Organization name |
Boston Children's Hospital
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| Department |
Oncology/Hematology
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE84129 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [G1ER ChIP-seq] |
| GSE84131 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation |
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| Relations |
| BioSample |
SAMN05363833 |
| SRA |
SRX1901619 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2227576_AC3-CHD7KO-E4-GATA2_peaks.narrowPeak.gz |
2.0 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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