|
| Status |
Public on May 06, 2022 |
| Title |
T-BLTL (Transforming Intermediate Prone) rep2 (ATAC-seq) |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblast (MEF)
treatment: mouse embryonic fibroblasts FACS-sorted after 5 days of Transfo
strain: C57BL/6
antibody: CD90.2-APC (eBioscience, 17-0902)
|
| Treatment protocol |
MEF are infected by OSKM retroviruses to induce Repro or by K-Ras G12V, shp53 lentiviruses combined with cMyc retroviral infection to induce Transfo and FACS-cell sorted after 5 days.
|
| Growth protocol |
MEF were generated from E13.5 Bcl11b-tdTomato mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol. iPS cells were grown in DMEM containing 15% KnockOut™ Serum Replacement, 1,000 U/ml leukemia inhibitory factor, 100U/ml PS, 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM NEAA and 0.1mM b-mercaptoethanol. Transformed cells were cultivated in the same medium than MEF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were freeze in medium containing 5% DMSO. ATAC-seq DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
T-BLTL_peaks.narrowPeak
T-BLTL_peaks.txt
T-BLTL_summits.bed
consensus_peak.bed
consensus_peak.counts
|
| Data processing |
Sequencing reads are aligned to the Ensembl mouse reference version 93 using bwa mem version 0.7.15
BAM files are Encode blacklist filtered and quality filtered at mapping quality 10.
Peaks are called with MACS2 version 2.1.1.20160309. Replicates are joined at this stage.
Peaks are merged with homer's mergePeak command for a consensus peak set
Coverage in consensus peak set is determined with multiBamCov from Bedtools2 version 2.25.0
Genome_build: mm9
Supplementary_files_format_and_content: peak counts and bed files
|
| |
|
| Submission date |
Aug 10, 2021 |
| Last update date |
Jul 06, 2022 |
| Contact name |
Fabrice Lavial |
| Organization name |
CRCL
|
| Street address |
28 rue Laennec
|
| City |
Lyon |
| ZIP/Postal code |
69008 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE137050 |
The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8 |
| GSE181799 |
Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b (ATAC-seq) |
|
| Relations |
| BioSample |
SAMN20695609 |
| SRA |
SRX11706767 |
