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Sample GSM5511558 Query DataSets for GSM5511558
Status Public on May 06, 2022
Title R-BHTH (Reprogramming Intermediate Refractory) rep1 (RNA-seq)
Sample type SRA
 
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblast (MEF)
treatment: mouse embryonic fibrobalsts FACS-sorted after 5 days of Repro
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. Malignant cells were cultivated in the same medium than MEF.
Extracted molecule total RNA
Extraction protocol RNAs were extracted with Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Sequenced reads were mapped to mm8 (release M19) whole genome and reads per gene were counted using STAR (ver. 2.5b).
Read counts were analyzed with R DeSeq2 package.
Genome_build: mm9
Supplementary_files_format_and_content: raw_count.csv: tab delimited csv file including raw counts for each sample
Supplementary_files_format_and_content: normalized_count.csv: tab delimited csv file including normalized counts for the each sample
Supplementary_files_format_and_content: model_fc.csv: tab delimited csv file including FC, p-value and adjusted p-value
 
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 GPL21103
Series (2)
GSE137050 The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8
GSE181800 Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b [RNA-seq]
Relations
BioSample SAMN20695673
SRA SRX11706776

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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