Comment[ArrayExpressAccession]	E-MTAB-1883
MAGE-TAB Version	1.1
Public Release Date	2013-10-17
Investigation Title	"Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription."
Comment[Submitted Name]	"Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription."
Experiment Description	"Transcriptome sequencing (RNA-seq) experiment of 14 human lymphoblastoid cell line samples from the 1000 Genomes sample set (http://www.1000genomes.org/). Dataset includes two parent-daughter trios (CEU and YRI populations) and additional eight unrelated individuals (CEU population). This accession contains raw and mapped RNA-seq read data, other assays in this study are available under accession E-MTAB-1884 (ChIP-seq,  https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1884) and E-MTAB-1885 (GRO-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1885).  "
Experimental Design	population based design	operator variation design
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[AEExperimentDisplayName]	RNA-seq of 14 human lymphoblastoid cell line samples from the 1000 Genomes sample set
Experimental Factor Name	individual	population
Experimental Factor Type	individual	population
Person Last Name	Kilpinen	Dermitzakis
Person First Name	Helena	Emmanouil
Person Mid Initials		T
Person Email	helena.kilpinen@unige.ch	emmanouil.dermitzakis@unige.ch
Person Phone	+41(0)223795550	+41(0)223795483
Person Fax	+41(0)223795706	+41(0)223795706
Person Address	"1 Rue Michel-Servet, 1211 Geneva, Switzerland"
Person Affiliation	"University of Geneva Medical School, Department of Genetic Medicine and Development"
Person Roles	submitter	investigator
PubMed ID	24136355
Publication Author List	Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis N, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET
Publication Title	Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription
Publication Status	in press
Protocol Name	P-MTAB-35315	P-MTAB-35316	P-MTAB-35317	P-MTAB-35318	P-MTAB-35319
Protocol Type	growth protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol
Protocol Description	"Lymphoblastoid cell lines were obtained from Coriell (http://ccr.coriell.org) and cultured in RPMI-1640 medium (Lonza) with 10% fetal calf serun (FCS). Frozen cells were thawed and transferred to T25 flasks containing 15 ml of medium. At a density of 0.3 x 10^6 cells/m cells were transferred to TubeSpin Bioreactor 50 tubes (TPP) in 5 ml of same medium containing 10% FCS and 0.1% Pluronic F-68 (Sigma-Aldrich). The cultures were agitated at 180 rpm with 5% CO2 and 85% humidity. When the cell density reached 2-3 x 10^6 cells/ml, the culture was diluted to 0.3 x 10^6 cells/ml and transferred to a 250-ml glass bottle. The culture was agitated at 110 rpm with 5% CO2 but no humidity. Eventually, the cells were scaled-up serially in 500-ml, 1-L, and 5-L glass bottles filled to a maximum of 40% of the nominal volume."	Total RNA was extracted from flash frozen cell pellets using the TRIzol Reagent (Invitrogen) according to manufacturer's instructions. No DNAse treatment of the RNA samples was performed. Total RNA quality was assessed with Bioanalyzer RNA 6000 Nano Kit (Agilent) and RNA quantity was measured with Qubit 2.0 (Invitrogen) RNA Broad range kit according to manufacturer's instructions.	Sequencing libraries were prepared with TruSeq RNA Sample Prep Kit v2 high-throughput protocol (Illumina) according to manufacturer's instructions.	"Sequencing was performed on the Illumina HiSeq 2000 platform using TruSeq PE Cluster Kit v3 (cluster generation) and TruSeq SBS Kit v3 (paired-end sequencing, read length 49 bp). Samples were multiplexed and sequenced either six or twelve samples per lane (Pilot2 and Pilot1 samples, respectively)."	Raw sequence reads were mapped against the standard hg19 build of the human reference genome using BWA 0.5.9 (http://bio-bwa.sourceforge.net) with default parameters for paired-end reads. Properly paired uniquely mapping reads with a mapping quality >= 10 were kept for further analyses.
Protocol Hardware				Illumina HiSeq 2000
Protocol Software					BWA 0.5.9
Comment[SecondaryAccession]	ERP004078
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR356365-ERR356378
SDRF File	E-MTAB-1883.sdrf.txt