|
| Status |
Public on Nov 10, 2022 |
| Title |
P19, WT, BMS641+BMS961, Day 4 |
| Sample type |
SRA |
| |
|
| Source name |
P19
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P19
cell type: carcinoma stem cells
genotype: WT
treatment: BMS641+BMS961
time: Day 4
|
| Treatment protocol |
For cell differentiation assays, all-trans retinoic acid (ATRA) was added to plates to a final concentration of 1 μM for different exposure times. For treatment with RAR subtype-specific agonists, cells were incubated with BMS961 (RARg-specific; 0.1 μM), BMS753 (RARa-specific; 1 μM), and/or BMS641 (RARb-specific; 0.1 μM). After four days of treatment with either of the aforementioned retinoids, medium was replaced by neurobasal medium (ThermoFisher Scientific ref: 21103049) supplemented with N2 (ThermoFisher Scientific ref: 17502048) and B27 devoid of vitaminA (ThermoFisher Scientific ref: 12587010) and cultured for 6 more days.
|
| Growth protocol |
P19 cells were grown in DMEM supplemented with 1 g/L glucose, 5% FCS, and 5% delipidated FCS. P19 EC cells were cultured in monolayer on gelatin-coated culture plates (0.1%).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from P19 cells treated with either ATRA or RAR-specific agonists, using the TRIzol RNA isolation reagent (ThermoFisher Scientific ref: 15596026).
RNA-sequencing libraries were produced with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (E7770).
poly-T captured mRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq files were qualified with the NGS-QC Generator tool (Mendoza-Parra et al, 2016b, 2013).
Reads from fastq files were mapped to the mouse mm9 reference genome using Bowtie 2.1.0 under default parameters.
Mapped reads were associated to known genes with featureCounts. RNA-Seq analyses were done with DESeq2 R-package.
Assembly: mm9
Supplementary files format and content: comma separated files containing differential expression levels (Log2) and confidence p-values (DeSeq2) relative to the WT_EtOHd2 control sample.
|
| |
|
| Submission date |
May 25, 2022 |
| Last update date |
Nov 10, 2022 |
| Contact name |
Marco Antonio Mendoza Parra |
| E-mail(s) |
mmendoza@genoscope.cns.fr
|
| Organization name |
Genoscope
|
| Street address |
2 Gaston Crémieux
|
| City |
Evry |
| ZIP/Postal code |
91000 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE204816 |
Synergistic activation of RARb and RARg-driven programs restores cell-types specialization during stem cell differentiation |
|
| Relations |
| BioSample |
SAMN28660197 |
| SRA |
SRX15457919 |
