|
| Status |
Public on Sep 02, 2019 |
| Title |
YL-STAG2-740-R1_HiC |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
protocol: HiC 2.0
enzyme: DpnII
cell type: Hematopoietic progenitor cells
genotype/variation: Stag2 knock-out
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Murine bone marrow cells were negatively selected for lineage markers using antibodies conjugated to magnetic beads and separated using EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies).
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. PMID: 28435001
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Mapping onto mm9 genome using cMapping pipeline (cMapping : https://github.com/dekkerlab/cMapping)
contact matrix files were generated using cWorld pipeline (cworlds-dekker : https://github.com/dekkerlab/cworld-dekker)
Genome_build: mm9
Supplementary_files_format_and_content: Insulation score calling, heatmap generation and compartment calling using cWorld pipeline (cworlds-dekker : https://github.com/dekkerlab/cworld-dekker)
|
| |
|
| Submission date |
Sep 02, 2018 |
| Last update date |
Sep 02, 2019 |
| Contact name |
Job Dekker |
| E-mail(s) |
Job.Dekker@umassmed.edu
|
| Phone |
508-856-4371
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Systems Biology
|
| Lab |
Dekker Lab
|
| Street address |
368 Plantation Street, AS5-1049
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE119366 |
Stag2 regulates hematopoietic differentiation and self-renewal through alterations in gene expression and topological control |
|
| Relations |
| BioSample |
SAMN09946138 |
| SRA |
SRX4633109 |
