|
| Status |
Public on May 06, 2022 |
| Title |
TC sh#Control rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblasts
strain: C57BL/6
shRNA: sh#Control
treatment: Malignant transformation induction
|
| Growth protocol |
TCs were cultivated in DMEM medium supplemented with 5% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted with Macherey-Nagel NucleoSpin RNA 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 2500 |
| |
|
| Description |
processed data file: raw_count_TC.txt
processed data file: normalized_count_TC.txt
processed data file: model_fc_TC.txt
|
| 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: mm8 (MGSCv36)
Supplementary_files_format_and_content: raw_count_TC.txt: Tab-delimited text file including raw counts for each sample.
Supplementary_files_format_and_content: normalized_count_TC.txt: Tab-delimited text file including normalized counts for the each sample.
Supplementary_files_format_and_content: model_fc_TC.txt: Tab-delimited text file including FC, p-value and adjusted p-value.
|
| |
|
| Submission date |
Jan 13, 2020 |
| 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 |
GPL17021 |
| Series (2) |
| GSE137050 |
The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8 |
| GSE143593 |
Identification of genes upregulated and downregulated in transformed cells (TCs) derived upon Atoh8 depletion |
|
| Relations |
| BioSample |
SAMN13839717 |
| SRA |
SRX7551172 |
