|Public on May 06, 2022
|MEF rep1 (ATAC-seq)
|mouse embryonic fibroblasts
|cell type: mouse embryonic fibroblast (MEF)
treatment: control mouse embryonic fibroblasts
|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.
|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.
|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
|Illumina NextSeq 500
|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 220.127.116.1160309. 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
Supplementary_files_format_and_content: peak counts and bed files
|Aug 10, 2021
|Last update date
|May 06, 2022
|28 rue Laennec
|The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8
|Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b (ATAC-seq)