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Sample GSM3897533 Query DataSets for GSM3897533
Status Public on Jun 20, 2019
Title DNA input_EXP#2
Sample type SRA
 
Source name cortical progenitor cells
Organism Mus musculus
Characteristics cell types: ES-cell derived A2 lox.Cre Bcl6 progenitor cells
differentiation day: day 12
chip antibody: none
Treatment protocol differentiation day 12, 24h Bcl6 induction using 1 µg.ml−1 Doxycline treatment
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 genomic DNA
Extraction protocol A2 lox.Cre Bcl6 cells were fixed with 1% formaldehyde in phosphate-buffered saline and then lysed, sonicated, and immunoprecipitated as described previously (Castro et al., 2011).
ChIP libraries were prepared according to the standard Illumina ChIP-seq protocol and were sequenced with the Genome Analyzer IIx (Illumina)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing all ChIP-seq experiments and sequencing datasets were pooled and aligned to mm10 mouse genome assembly using Bowtie
Peaks were called using MACS with standard parameters and default cutoff P value <10e-5.
Target genes associated with peaks were identified by GREAT version 3.0
Search for an enrichment of Bcl6 matrices in the MACS-called ChIP peaks was performed using i-cisTarget using a promoter-only database.
Genome_build: mm10
Supplementary_files_format_and_content: gene list associated with Chip-seq.txt
 
Submission date Jun 19, 2019
Last update date Jun 20, 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 GPL11002
Series (2)
GSE132964 Bcl6 binding sites in in vitro cortical progenitors [ChIP-Seq]
GSE133032 Bcl6 binding sites and neurogenic activity in in vitro cortical progenitors
Relations
BioSample SAMN12096669
SRA SRX6095750

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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