Comment[ArrayExpressAccession]	E-GEOD-48591
MAGE-TAB Version	1.1										
Public Release Date	2014-06-22
Investigation Title	Runx3 regulated genes in splenic CD4+ dendritic cells										
Comment[Submitted Name]	Runx3 regulated genes in splenic CD4+ dendritic cells
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series										
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	Groner										
Person First Name	Yoram										
Person Email	yoram.groner@weizmann.ac.il										
Person Affiliation	Weizmann institute of science										
Person Address	Molecular genetics, Weizmann institute of science, P.O.B 26, Rehovot, istael, Israel										
Person Roles	submitter										
Protocol Name	P-GSE48591-1	P-GSE48591-7	P-GSE48591-8	P-GSE48591-10	P-GSE48591-4	P-GSE48591-6	P-GSE48591-3	P-GSE48591-2	P-GSE48591-5	P-GSE48591-11	P-GSE48591-9
Protocol Description	Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization. MoGene-1_0-st-v1.r4.pgf MoGene-1_0-st-v1.na31.mm9.transcript.csv ID_REF =  VALUE = Log2 normalized gene level expression values from RMA	Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)	Samples were hybridized using Affymetrix hybridization kit materials and protocol. Fluidics washing is FS450_0007	FACS sorted Esam polulation on CD11c+/MHCII+ on Esam/CD4/CD8	FACS sorted Esam polulation on CD11c+/MHCII+ on CD4/CD8	Total RNA was isolated using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions, which included a DNase step.	Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 40ul of anti-Runx3 Ab were added to 15 mL of diluted, fragmented chromatin; whole cell extract fragmented chromatin served as control. DNA was purified using QIAquick spin columns (QIAGEN). For ChIP-seq analysis, indexed CiHP-seq libraries were prepared as published Blecher-Gonen et al. Nature Protocols 8, 539–554 (2013). Illumina sequencing of short reads (50 bp) was performed in one lane of Hiseq 2000 using v3 clustering and sequencing reagents.	Two biological replicate ChIP-Seq experiments were conducted for detection of Runx3-bound genomic regions using in-house anti Runx3 Ab and 30x106 positive CD11c MACS isolated (Miltenyi Biotec) DC. These cells were further purified by FACS to CD11chiMHCII+CD4+ cDC subset, collected from approximately 15 mice. DC were freshly sorted, fixed and frozen -80c.	Mouse CD4+ splenic dendritic cells freshly isolated and facs sorted.	Mouse Esam splenic dendritic cells freshly isolated and facs sorted.	Affymetrix Gene ChIP Scanner 3000 7G
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	sample treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	growth protocol	growth protocol	array scanning protocol
Experimental Factor Name	CHIP ANTIBODY	GENOTYPE	STRAIN								
Experimental Factor Type	chip antibody	genotype	strain								
Publication Title	Transcriptional reprogramming of CD11b+Esam(hi) dendritic cell identity and function by loss of Runx3.										
Publication Author List	Dicken J, Mildner A, Leshkowitz D, Touw IP, Hantisteanu S, Jung S, Groner Y										
PubMed ID	24204843										
Publication DOI	10.1371/journal.pone.0077490										
Comment[SecondaryAccession]	GSE48591										
Comment[GEOReleaseDate]	2014-06-22										
Comment[ArrayExpressSubmissionDate]	2013-07-08										
Comment[GEOLastUpdateDate]	2014-06-24										
Comment[AEExperimentType]	transcription profiling by array										
Comment[AEExperimentType]	ChIP-seq										
SDRF File	E-GEOD-48591.hyb.sdrf.txt	E-GEOD-48591.seq.sdrf.txt