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Sample GSM3592669 Query DataSets for GSM3592669
Status Public on Feb 07, 2019
Title KrasG12D ubChIP-seq (2)
Sample type SRA
 
Source name Myeloid Progenitor Cells
Organism Mus musculus
Characteristics genotype: scl-Cre-ERT +; BcorWT/y;KrasG12D/WT
tissue: Bone Marrow
cell type: Myeloid Progenitor Cells
chip antibody: H2AK119ub (Cell Signalling Technology, 8240S, lot 2)
Extracted molecule genomic DNA
Extraction protocol Donor-derived 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 K2
Data processing Sample QC was first 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(v2.3.3) to the mouse reference genome (GRCm38/mm10)
Read counting over genomic regions, filtering, normalisation and computation of statistical significance was performed with R package Csaw (v1.10.0). TDF files were generated with IGVTools (v2.3.95)
Genome_build: mm10
Supplementary_files_format_and_content: Browser viewable TDF 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)
GSE126177 Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [BcorKrasChIP-seq]
GSE126264 Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis
Relations
BioSample SAMN10881438
SRA SRX5342471

Supplementary file Size Download File type/resource
GSM3592669_K2ub_S5_R1_001.fastq.gz.sam.sorted.bam.rmdup.bam.tdf 258.5 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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