|
| Status |
Public on Jun 09, 2022 |
| Title |
ChIPseq_H3K27ac_stage2 |
| 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 line: Primary mouse bone marrow cells
Stage: 2
chip antibody: Millipore 07-360
|
| Treatment protocol |
None
|
| 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 |
(ChIP-seq) ChIP experiments were carried out following a standard protocol in the lab (PubMed ID: 30224650)
(RNA-seq) RNA was extracted with the RNeasy kit (Qiagen) following manufacturer's instructions
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq analysis: Alignment: Sequence reads of the samples were mapped to the mouse genome (mm10) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles were normalized by the total number of reads of each sample.
RNA-seq analysis: Alignment: Sequence reads were mapped against the mm10 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. RNA-seq genome-wide profiles were normalized by the total number of reads of each sample in plus and minus strands.
Genome_build: mm10
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)
|
| |
|
| Submission date |
Jun 04, 2020 |
| Last update date |
Jun 09, 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 |
SAMN15104891 |
| SRA |
SRX8473421 |
