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Sample GSM1888844 Query DataSets for GSM1888844
Status Public on Sep 21, 2015
Title Mxplus_Flt3ITD_ATAC_2
Sample type SRA
Source name c-Kit+ cells purified from bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
cell type: c-Kit+ cells
genotype: Flt3-ITD
Growth protocol Whole bone marrow from individual mice was positively selected for Cd117 (c-Kit) using antibody-conjugated magnetic beads (Cd117 microbeads, Miltenyi Biotec Inc).
Extracted molecule genomic DNA
Extraction protocol Chromatin accessibility assays utilizing the bacterial Tn5 transposase were performed as described (Buenrostro et al., 2013) with minor modifications. Cells (50,000/sample) were washed twice in cold PBS, and lysed in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition reactions were set up with the Illumina Nextera DNA Preparation kit (Illumina #FC-121-1030) and incubated at 37 degrees for 60 minutes. Genomic DNA was then purfied, and libraries were PCR-amplified with individual bar-coded PCR primers.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Description Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and single floxed Smc3 allele
Data processing Library strategy: ATAC-seq
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset. Peak-calling was performed using ZINBA with a window size of 300bp and an offset of 75bp
Genome_build: mm9
Supplementary_files_format_and_content: BED files: for all samples, aligned sequences processed through zinba and enriched regions were outputted in BED format
Submission date Sep 18, 2015
Last update date May 15, 2019
Contact name James Bradner
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Bradner Lab
Street address 450 Brookline
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL19057
Series (2)
GSE73215 Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis [ATAC-Seq]
GSE73218 Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis
BioSample SAMN04096884
SRA SRX1262034

Supplementary file Size Download File type/resource
GSM1888844_Mxplus_Flt3ITD_ATAC_2.peaks.bed.gz 877.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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