NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3898658 Query DataSets for GSM3898658
Status Public on Jun 20, 2019
Title control_differentiation #4
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 D4-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 SAMN12096789
SRA SRX6095790

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap