MAGE-TAB Version	1.1			
Public Release Date	2012-11-06			
Investigation Title	small RNA-sequencing of 452 lymphoblastoid cell lines from the 1000 Genomes			
Experiment Description	This RNA sequencing data set of 465 human lymphoblastoid cell line samples from the CEU, FIN, GBR, TSI and YRI populations from the 1000 Genomes sample collection was created by the Geuvadis consortium (www.geuvadis.org, http://www.geuvadis.org/web/geuvadis/our-rnaseq-project). The data is under embargo until the first publication by the investigators in early 2013. This accession contains small RNA sequencing data, and mRNA data from the same samples are available under accession E-GEUV-1. 			
Person Last Name	Kurbatova	Lappalainen	Dermitzakis	
Person First Name	Natalja	Tuuli	Emmanouil	
Person Mid Initials				
Person Email	natalja@ebi.ac.uk	Tuuli.Lappalainen@unige.ch	emmanouil.dermitzakis@unige.ch	
Person Affiliation	EBI	UNIGE	UNIGE	
Person Phone				
Person Fax				
Person Address				
Person Roles	submitter	investigator	investigator	
Experimental Design	population based design	operator variation design		
Experimental Design Term Accession Number	EFO_0001430	EFO_0001772		
Experimental Design Term Source REF	EFO	EFO		
Protocol Name	P-GEUV-1	P-GEUV-2	P-GEUV-3	P-GEUV-4
Protocol Description	For information about the sample characteristics, populations, and available genotype information, see http://www.1000genomes.org and http://ccr.coriell.org . EVB transformed lymphoblastoid cell lines (LCLs) were shipped to ECACC (European COllection of Cell Cultures) as live cultures (06/2011 - 09/2011), in batches of ~ 30 samples from Coriell (GBR,FIN & TSI) and 2 x ~90 samples (CEU & YRI) from University of Geneva. In ECACC, the cell lines were cultured to approximately 1.2 x 10e8 cells (06/2011-10/2011). Snap frozen pellets of 2 x 10e7 cells were produced from proliferating cultures without additives. 	Total RNA was extracted from cell pellets in the University of Geneva using the TRIzol Reagent (Ambion) according to the manufacturer's guidelines. No DNAse treatment was done to the RNA samples. RNA quality was assessed by Agilent Bioanalyzer RNA 6000 Nano Kit, and RNA quantity was measured by Qubit 2.0 (Invitrogen) using the RNA Broad range kit according to the manufacturer's instructions. 	Sample processing for sequencing was done in a random order in each of the seven laboratories. 5 samples were sequenced in every laboratory. Library preparation was done with TruSeq Sm RNA Sample Prep. 	The sequencing platform was Illumina HiSeq. The cluster generation kit was TruSeq PE Cluster Kit v3, and the sequencing kit was TruSeq SBS Kit v3. 36 bp single-end sequencing was done to the depth of about 3M total reads.
Protocol Software				
Protocol Hardware				Illumina HiSeq 2000
Protocol Contact				
Protocol Type	growth protocol	nucleic acid extraction protocol	cDNA library construction protocol	nucleic acid sequencing protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO
Protocol Term Accession Number	EFO_0003789	EFO_0002944	EFO_0004187	EFO_0004170
Experimental Factor Name	population	laboratory		
Experimental Factor Type	ethnic group	laboratory		
Experimental Factor Term Source REF	EFO	EFO		
Experimental Factor Term Accession Number	EFO_0001799	EFO_0004907 		
Comment[Submitted Name]	small RNA-sequencing of 465 lymphoblastoid cell lines from the 1000 Genomes			
Term Source Name	NCBI Taxonomy	EFO		
Term Source Version		2.29		
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/	http://www.ebi.ac.uk/efo		
Comment[AEExperimentType]	microRNA profiling by high throughput sequencing			
Comment[SecondaryAccession]	ERP001941			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR187488-ERR187939
Comment[ArrayExpressAccession]	E-GEUV-2
SDRF File	E-GEUV-2.sdrf.txt			
