GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE46119 Query DataSets for GSE46119
Status Public on Apr 02, 2014
Title Mapping of Ikaros and RBPJ binding sites in the mouse T cell leukemia cell line T29
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The transcription factor Ikaros represses Notch signaling. Since Ikaros and Notch treanscriptional mediator RBPJ both recognize sequences that contain the same core TGGGAA motif, it was hypothesized that Ikaros represses Notch signaling by targeting Notch response elements and competing with RBPJ for their binding. Here we used the mouse T-cell leukemia cell line T29 to compare the genomic binding profiles of Ikaros and RBPJ by ChIP-seq.
Overall design The T29 cell line is derived from a Ikaros-deficient T-cell leukemia (Dumortier et al, MCB 26, 209-220, 2006) and exhibits strong Notch activation. We performed two chip-seq experiments with an anti-RBPJ antibody to map RBPJ binding sites. To map Ikaros binding sites, we engineered a T29-derived cell line that expresses a fusion protein between Ikaros and the ligand binding domain of the estrogen receptor (Ik1-ER) which is activated by addition of 4-hydroxy-tamoxifen (4OHT). We used an anti-Ikaros antibody to map the sites bound by Ik1-ER after treatment of the cells with 4OHT. Sequencing were performed with the Illumina GAII sequencer as as single end 36 base pair reads.
Contributor(s) Kastner P
Citation(s) 24643801
Submission date Apr 16, 2013
Last update date May 15, 2019
Contact name Susan Chan
Phone 33 3 88 65 34 72
Organization name IGBMC
Street address 1, rue Laurent Fries
City Illkirch
ZIP/Postal code 67404
Country France
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (6)
GSM1123942 input sample for RBPJ ChIP experiment 1
GSM1123943 input sample for RBPJ ChIP experiment 2
GSM1123944 RBPJ ChIP sample 1
BioProject PRJNA197303
SRA SRP021116

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46119_RAW.tar 626.6 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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