Comment[ArrayExpressAccession]	E-GEOD-46913
MAGE-TAB Version	1.1													
Public Release Date	2014-06-03
Investigation Title	Transcripts differentially expressed in healthy blood mDCs compared to healthy monocytes													
Comment[Submitted Name]	Transcripts differentially expressed in healthy blood mDCs compared to healthy monocytes
Experiment Description	To directly compare the SLE monocyte transcriptional program with that of blood mDC precursors, we purified lineage HLA-DRhighCD11chigh mDCs and CD14+ monocytes from the blood of five healthy donors. Their gene expression profiles were then compared to those of blood SLE monocytes. An unsupervised clustering analysis of transcripts present in >20% of the samples classified healthy monocytes, SLE monocytes and healthy mDCs into three well defined groups. A supervised analysis was then performed to find genes: 1) differentially expressed in healthy mDCs compared to monocytes; 2) shared by healthy blood mDCs and SLE blood monocytes. To directly compare the SLE monocyte transcriptional program with that of blood mDC precursors, we purified lineage HLA-DRhighCD11chigh mDCs and CD14+ monocytes from the blood of five healthy donors. Their gene expression profiles were then compared to those of blood SLE monocytes. An unsupervised clustering analysis of transcripts present in >20% of the samples classified healthy monocytes, SLE monocytes and healthy mDCs into three well defined groups. A supervised analysis was then performed to find genes: 1) differentially expressed in healthy mDCs compared to monocytes; 2) shared by healthy blood mDCs and SLE blood monocytes.													
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	Baldwin	Rodriquez-Pla	Patel	Maecker	Rossello-Urgell	Baldwin	Bennett	Cantrell	Punaro	Gotte	Nassi	Palucka	Banchereau	Pascual
Person First Name	Nicole	Alicia	Pinakeen	Holden	Jose	Nicole	Lynda	Victoria	Marilynn	Alisa	Lorien	Karolina	Jacques	Virginia
Person Mid Initials												A		
Person Email	geo@ncbi.nlm.nih.gov													
Person Affiliation	BIIR													
Person Address	BIIR, 3434 Live Oak, Dallas, USA													
Person Roles	submitter													
Protocol Name	P-GSE46913-1	P-GSE46913-5	P-GSE46913-6	P-GSE46913-2	P-GSE46913-3	P-GSE46913-4	P-GSE46913-7							
Protocol Description	To analyze the data from monocytes from untreated and treated SLE patients, 5 samples in each data set were used for final analysis, and compared to 5 samples from healthy donors.  Data were normalized to this set of healthy controls.  For each set of experiments, unsupervised clustering of samples was performed using the list of genes present in at least one sample to rule out technical variability.  For supervised analysis, an Affymetrix flag call of M-bM-^@M-^XpresentM-bM-^@M-^Y in 3 out of 5 samples from each cohort was used to designate the filter for a reliable intensity measurement from each individual gene chip.  These two lists combined were used as a quality control measure for class comparison, which was performed using a non- parametric ranking statistical analysis test (Mann Whitney) as well as a 2-fold difference in the average normalized value of healthy to test set. ID_REF =  VALUE = MAS 5.0 signal	RNA was labeled using the GeneChipM-. Two-Cycle Target Labeling kit (Affimetrix, Santa Clara, CA) following the manufacturerM-bM-^@M-^Ys recommended procedures	cRNA was fragmented and hybridized to the HG-U133A & HG-U133B Affymetrix GeneChipM-. arrays that contain 45,000 probe sets at 45 M-bM-^AM-0C for 16 hours	none, healthy monocytes.	none	mDCs and monocytes from healthy volunteers were sorted on a FACSAriaM-. (BD Bioscience, Franklin Lakes, NJ) as Lineage- CD11c+HLA-DR+ and CD14+HLA-DR+ cells, respectively. RNA was extracted from isolated cells using either the RNeasyM-. Mini Kit (Qiagen, Valencia, CA), if >5x105 were recovered, or PicoPureTM RNA Isolation Kit (Molecular Devices Corporation, Sunnyvale, CA) when <5x105 cells were recovered	GeneChip arrays were washed, stained, and scanned according to protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA)							
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol							
Experimental Factor Name	SUBJECT	CELL TYPE												
Experimental Factor Type	subject	cell type												
Publication Title	IFN Priming Is Necessary but Not Sufficient To Turn on a Migratory Dendritic Cell Program in Lupus Monocytes.													
Publication Author List	Rodriguez-Pla A, Patel P, Maecker HT, Rossello-Urgell J, Baldwin N, Bennett L, Cantrell V, Baisch J, Punaro M, Gotte A, Nassi L, Wright T, Palucka AK, Banchereau J, Pascual V													
PubMed ID	24829414													
Publication DOI	10.4049/jimmunol.1301319													
Comment[SecondaryAccession]	GSE46913													
Comment[GEOReleaseDate]	2014-06-03													
Comment[ArrayExpressSubmissionDate]	2013-05-14													
Comment[GEOLastUpdateDate]	2014-06-03													
Comment[AEExperimentType]	transcription profiling by array													
SDRF File	E-GEOD-46913.sdrf.txt