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Sample GSM3592628 Query DataSets for GSM3592628
Status Public on Feb 07, 2019
Title 20w BcorΔE9-10 H3K27me3 Chip-seq (2)
Sample type SRA
 
Source name Myeloid Progenitor Cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: scl-Cre-ERT +; Bcorfl/y
tissue: Bone Marrow
cell type: Myeloid Progenitor Cells
treatment: Tamoxifen IP
chip antibody: H3K27me3 (Millipore,07449, lot 2736613)
Treatment protocol Mice aged 3-6 months were administered 1mg tamoxifen for 5 consecutive days
Extracted molecule genomic DNA
Extraction protocol Lin-cKIT+Sca-1- myeloid progenitor cells were isolated from the BM of experimental mice by FACS. Nuclei were isolated from cross-linked cells and sonicated to shear chromatin, then histone-DNA complexes were immunoprecipitated using relevant antibodies.
DNA libraries were prepared using the KAPA Hyper Prep Kit for Illuminaplatforms (Kapa Biosystems) and the SeqCap Adapter Kit (Roche) following vendor’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description H3K27me3-B2
Data processing Sample QC was performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The ChIP-sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using bowtie2 to the mouse reference genome (GRCm38/mm10)
Peak calling was performed with MACS (v2.1.1) and BigWigs were created with deeptools(v2.5.3)
Normalisation, enrichment over genomic regions, and computation of statistical significance were performed with R package Csaw (v1.10.0).
Genome_build: mm10
Supplementary_files_format_and_content: Peaks files
Supplementary_files_format_and_content: bigWig Files
 
Submission date Feb 06, 2019
Last update date Feb 12, 2019
Contact name Madison Kelly
E-mail(s) mjk4002@med.cornell.edu
Organization name Weill Cornell Medicine
Street address 413 E69th Street
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL19057
Series (2)
GSE126173 Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [20wChiP-seq]
GSE126264 Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis
Relations
BioSample SAMN10881088
SRA SRX5342430

Supplementary file Size Download File type/resource
GSM3592628_H3K27me3-B2_S9_R1_001.fastq.gz.sam.sorted.bam.rmdup.bam.bw 57.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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