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Sample GSM3901649 Query DataSets for GSM3901649
Status Public on Jan 01, 2023
Title G1ER_CHD7-KO_PolII-phospho-serineII Input rep1
Sample type SRA
 
Source name G1ER cell line
Organism Mus musculus
Characteristics cell line: G1ER
tissue: erythroblasts
genotype: Chd7-/-
antibody: none
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).
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
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.
 
Submission date Jun 23, 2019
Last update date Jan 01, 2023
Contact name Leonard Zon
E-mail(s) zon@enders.tch.harvard.edu
Organization name Boston Children's Hospital
Department Oncology/Hematology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
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
Relations
BioSample SAMN12122840
SRA SRX6352564

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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