|
| Status |
Public on May 06, 2022 |
| Title |
T-BHTH (Transforming 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 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% 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. 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 |
SAMN20695677 |
| SRA |
SRX11706780 |
