|
| Status |
Public on Sep 21, 2015 |
| Title |
Mxplus_Smc3het_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: Smc3 del/+
|
| 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 Flt3-ITD 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 |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN04096886 |
| SRA |
SRX1262036 |
