|
| Status |
Public on Jun 09, 2022 |
| Title |
HiC_stage0_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow lineage negative hematopoietic stem/progenitor cells from 8-10-week-old female mice
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary mouse bone marrow cells
Stage: stage 0
|
| Growth protocol |
Bone marrow lineage negative hematopoietic stem/progenitor cells from 8-10-week-old female mice were harvested and infected with high-titer retroviruses expressing either an empty PINCO-3xFlag vector or a PINCO–PML-RARa-3xFlag vector carrying human PML-RARa. GFP+ cells transformed with empty vector or PML-RARa-3xFlag vector were sorted by FACS and correspond to stage 0 and stage I, respectively. Stage I cells were then plated in methylcellulose supplemented with cytokines and stem cell factor, and serially re-plated for 2 weeks (stage II) and 4 weeks (stage III). In parallel, approximately 1 million of GFP+ PML-RARa-3xFlag transduced lineage negative cells (stage I) were transplanted via tail vein injection into lethally irradiated (9 Gy) syngeneic mice (129SvEv) . The animals were monitored periodically for signs of disease and presence of blasts as evaluated by complete blood counts (CBC) and peripheral blood smears. Leukemic mice were humanely euthanized and bone marrow blasts (Mac1+) were isolated for subsequent experiments (stage IV).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547).
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HiC experiment
|
| Data processing |
TADbit’s fragment based mapping module (aligning with GEM) with the default parameters was used to align reads. TADbit’s filtering module was used to filter out non-informative contacts (self-circle, dangling ends, extra-dangling ends, errors, duplicated and random breaks). PUBMED: TADbit (28723903) and GEM (26094690)
Contact matrices were obtained and poor bins (containing low counts) were filtered out using TADbit’s routines. Raw and normalized counts at 100Kb resolution are stored as tab-separated files with chromosome in first column, coordinates of first bin as second column, and number of contacts to the second bin of the same chromosome in the third column.
Assembly: mm10
Supplementary files format and content: Raw and normalized interaction matrices are stored in the following format: chromosome, left-bin and right-bin positions (only cis interactions are included)
|
| |
|
| Submission date |
Mar 18, 2022 |
| Last update date |
Jun 10, 2022 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE151837 |
PML-RARa induces dynamic changes in genome architecture during leukemic transformation |
|
| Relations |
| BioSample |
SAMN26798333 |
| SRA |
SRX14488011 |
