|
| Status |
Public on Jun 20, 2019 |
| Title |
DNA input_EXP#1 |
| 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 |
SAMN12096671 |
| SRA |
SRX6095748 |
