Comment[ArrayExpressAccession]	E-MTAB-2068
MAGE-TAB Version	1.1
Investigation Title	Andersson_et_al_2013
Comment[Submitted Name]	Andersson_et_al_2013
Experiment Description	LGL leukemia is chronic clonal lymphoproliferative disorder, characterized by expansion of cytotoxic CD8+ T-cells or NK-cells. We compared gene expression of 2 LGL leukemia patients with STAT3 mutation (Patients 11 and 12) and 2 LGL leukemia patients without STAT3/STAT5b mutation (Patients 9 and 10) with CD8 and CD4 samples from healthy controls to assess different gene expression patterns between samples.
Experimental Design	disease_state_design	in_vitro_design	co-expression_design
Comment[AEExperimentType]	transcription profiling by array
Comment[AEExperimentDisplayName]	Transcription profiling by array of human CD8-positive T cells from patients with LGL leukemia
Experimental Factor Name	disease	genotype	cell type
Experimental Factor Type	disease	genotype	cell type
Quality Control Type	Biological replicate
Quality Control Term Source REF	EFO
Public Release Date	2013-11-14
Person Last Name	Andersson	Mustjoki
Person First Name	Emma	Satu
Person Mid Initials	I
Person Email	emma.i.andersson@helsinki.fi	satu.mustjoki@helsinki.fi
Person Phone
Person Address
Person Affiliation	Hematology Research Unit, Department of Medicine, University of Helsinki	Hematology Research Unit, Department of Medicine, University of Helsinki
Person Roles	submitter	Corresponding author
PubMed ID
Publication Author List	Emma I Andersson, Hanna L M Rajala, Samuli Eldfors, Pekka Ellonen, Thomas Olson, Andres Jerez, Michael J. Clemente, Olli Kallioniemi, Kimmo Porkka, Caroline Heckman, Thomas P. Loughran Jr.,  Jaroslaw P. Maciejewski and Satu Mustjoki
Publication Title	Novel Somatic Mutations in Large Granular Lymphocytic Leukemia affecting the STAT-pathway and T-cell activation
Publication Status	accepted
Protocol Name	P-MTAB-36035	P-MTAB-36036	P-MTAB-36037	P-MTAB-36038	P-MTAB-36039	P-MTAB-36040
Protocol Type	Sample collection method	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning protocol	normalization data transformation protocol
Protocol Description	Mononuclear cells (MNCs) were separated from peripheral blood (PB) using Ficoll gradient separation (GE Healthcare) and CD8+ T cells were further separated with magnetic beads separation: PB MNCs were labeled with CD8 MicroBeads (Miltenyi Biotech) according to instructions by the manufacturer and separated with an AutoMACS cell sorter (Miltenyi Biotech).  NK cells were negatively selected using Dynabeads Untouched Human NK cells-kit (Invitrogen). Purity of the sorted fractions was confirmed by flow cytometry (FACSAria, Becton Dickinson).	RNA was isolated from fresh or frozen sorted MNCs or from whole blood samples using miRNeasy kit (Qiagen).	Standard Illumina labelling protocol	Standard Illumina hybridization protocol	iScan, Genome Studio software v2011.1 (Illumina)	Microarray data was normalized using Chipster software, according to Smyth GK, Speed T. Normalization of cDNA microarray data. Methods. 2003;31:265-273.; Ritchie ME, Silver J, Oshlack A, et al. A comparison of background correction methods for two-colour microarrays. Bioinformatics. 2007;23:2700-2707.
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Term Source Name	EFO	ArrayExpress
Term Source File	http://www.ebi.ac.uk/efo	http://www.ebi.ac.uk/arrayexpress
SDRF File	E-MTAB-2068.sdrf.txt