NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5511550 Query DataSets for GSM5511550
Status Public on May 06, 2022
Title T-BHTH (Transforming Intermediate Refractory) rep1 (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% KnockOutā„¢ 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-BHTH_peaks.narrowPeak
T-BHTH_peaks.txt
T-BHTH_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 SAMN20695610
SRA SRX11706768

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap