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Sample GSM5502593 Query DataSets for GSM5502593
Status Public on May 06, 2022
Title repro_10d (scRNA-seq)
Sample type SRA
 
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblasts
strain: C57BL/6
treatment: mouse embryonic fibroblasts after 10 days of Repro
treatment time: 10 days
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 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 total RNA
Extraction protocol Cell suspension was mixed with master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell G Chip. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
10x Genomics Chromium 3' v3.1 Single Cell Gene Expression Kit protocol was followed according to manufacturer instructions.
scRNAseq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Bcl2 files were transormed to fastq files with cellranger mkfastq v 5.0.1.
Alignment, filtering and quantification were done with cellranger count v 5.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Outputs from cellranger count: barcodes, features and matrix files.
 
Submission date Aug 04, 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 GPL24247
Series (2)
GSE137050 The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8
GSE181451 Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b [scRNA-seq]
Relations
BioSample SAMN20571152
SRA SRX11647384

Supplementary file Size Download File type/resource
GSM5502593_repro_10d_barcodes.tsv.gz 24.4 Kb (ftp)(http) TSV
GSM5502593_repro_10d_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM5502593_repro_10d_matrix.mtx.gz 90.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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