|
| Status |
Public on Jun 20, 2019 |
| Title |
control_differentiation #3 |
| Sample type |
SRA |
| |
|
| Source name |
cortical progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell types: ES-cell derived A2 lox.Cre Bcl6 progenitor cells
treatment: DMSO
differentiation day: day 12
|
| Treatment protocol |
differentiation day 12, 24h Bcl6 induction using 1 µg.ml−1 Doxycline treatment or DMSO (control)
|
| Growth protocol |
The A2 lox.Cre Bcl6 cell lines, tetracyclin-inducible Bcl6 ICE (A2lox.Cre) mouse Embryonic Stem Cells were routinely propagated on irradiated mouse embryonic fibroblasts in DMEM supplemented with 15% ESC-certified fetal bovine serum (vol/vol), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 50 U.ml−1 penicillin/ streptomycin and 10E3 U.ml−1 mouse Leukemia Inhibitor Factor. For differentiation, A2 lox.Cre Bcl6 mouse ESCs were plated at low density (20 × 10E3 ml−1) on gelatin-coated 5-cm dishes (day -1). At day 0, the ES medium was changed to DDM medium. At day 2, DDM was supplemented with cyclopamine (400 ng/mL) and the medium was replenished every 2 days. After 10 days, medium was switched back to DDM (Gaspard et al., 2009).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted using the QIAGEN RNeasy mini kit
the indexed cDNA libraries were prepared using the TruSeq stranded mRNA Library Preparation kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
D3-Control
|
| Data processing |
paired-end reads per sample were mapped against the mouse reference genome using STAR 2.5.3a
gene level counts were obtained using HTSeq 0.9.1
level of differential gene expression was calculated using EdgeR 3.20.1
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and normalized abundance measurements
|
| |
|
| Submission date |
Jun 19, 2019 |
| Last update date |
Jun 21, 2019 |
| Contact name |
Pierre Vanderhaeghen |
| E-mail(s) |
pierre.vanderhaeghen@kuleuven.vib.be
|
| Organization name |
VIB-KU Leuven
|
| Department |
Center for Brain & Disease Research
|
| Lab |
Stem cell and Developmental neurobiology
|
| Street address |
O&N4 Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE133031 |
Bcl6 neurogenic activity in in vitro cortical progenitors [RNA-Seq] |
| GSE133032 |
Bcl6 binding sites and neurogenic activity in in vitro cortical progenitors |
|
| Relations |
| BioSample |
SAMN12096791 |
| SRA |
SRX6095788 |
