Comment[ArrayExpressAccession]	E-GEOD-46119
MAGE-TAB Version	1.1		
Public Release Date	2014-04-02
Investigation Title	Mapping of Ikaros and RBPJ binding sites in the mouse T cell leukemia cell line T29		
Comment[Submitted Name]	Mapping of Ikaros and RBPJ binding sites in the mouse T cell leukemia cell line T29
Experiment Description	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. 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.		
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl	
Person Last Name	Chan	Kastner	
Person First Name	Susan	Philippe	
Person Email	scpk@igbmc.fr		
Person Affiliation	IGBMC		
Person Phone	33 3 88 65 34 72		
Person Fax	33 3 88 65 32 01		
Person Address	IGBMC, 1, rue Laurent Fries, Illkirch, France		
Person Roles	submitter		
Protocol Name	P-GSE46119-3	P-GSE46119-1	P-GSE46119-2
Protocol Description	Illumina pipeline v1.3 to v1.6 are used for basecalling. Sequence reads were mapped to reference genome mm9/NCBI37 using GERALD. Only 2 mismatch reads were kept for further analysis. Genome_build: mm9 Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)	T29-IKER cells were treated with 4OHT (100 nM) for 24h.	ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single M-bM-^@M-^XAM-bM-^@M-^Y nucleotide was added to the 3M-bM-^@M-^Y ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98M-0C; [10 sec at 98M-0C, 30 sec at 65M-0C, 30 sec at 72M-0C] x 14 cycles; 5 min at 72M-0C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol
Experimental Factor Name	CHIP ANTIBODY	CELL TYPE	
Experimental Factor Type	chip antibody	cell type	
Publication Title	The tumor suppressor Ikaros shapes the repertoire of notch target genes in T cells.		
Publication Author List	Geimer Le Lay AS, Oravecz A, Mastio J, Jung C, Marchal P, Ebel C, DembM-oM-?M-=lM-oM-?M-= D, Jost B, Le Gras S, Thibault C, Borggrefe T, Kastner P, Chan S		
PubMed ID	24643801		
Publication DOI	10.1126/scisignal.2004545		
Comment[SecondaryAccession]	GSE46119		
Comment[GEOReleaseDate]	2014-04-02		
Comment[ArrayExpressSubmissionDate]	2013-04-16		
Comment[GEOLastUpdateDate]	2014-04-02		
Comment[AEExperimentType]	ChIP-seq		
Comment[SecondaryAccession]	SRP021116		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR828662-SRR828667		
SDRF File	E-GEOD-46119.sdrf.txt