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Sample GSM5511489 Query DataSets for GSM5511489
Status Public on May 06, 2022
Title MEF, Transfo d5 rep2 (ATAC-seq)
Sample type SRA
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblast (MEF)
treatment: 5 days of Transfo (viral induction of K-RasG12V + cMyc + shp53)
strain: C57BL/6
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.
Growth protocol MEF were generated from E13.5 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.
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
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 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
Submission date Aug 10, 2021
Last update date May 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
GSE181796 Chromatin accessibility after 5 days of reprogramming and transformation
BioSample SAMN20695454
SRA SRX11706688

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

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