7 protocols
AccessionNameType
P-GEUV-4
nucleic acid sequencing protocol
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.
P-GEUV-3
cDNA library construction protocol
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.
P-GEUV-2
nucleic acid extraction protocol
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.
P-GEUV-1
growth protocol
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.
P-GEUV-7
high throughput sequence alignment protocol
The reads were mapped to the human hg19 reference genome (autosomes+X+Y+M) with the GEM mapper v 1.349 mapping entire reads, and split mapping the unmapped reads (see http://www.geuvadis.org/web/geuvadis/our-rnaseq-project for settings). In the bam files, mapping quality is scored as follows: 1) Matches which are unique, and do not have any subdominant match: 251 >= MAPQ >= 255, XT=U ; 2) Matches which are unique, and have subdominant matches but a different score: 175 >= MAPQ >= 181, XT=U ; 3) Matches which are putatively unique (not unique, but distinguishable by score): 119 >= MAPQ >= 127, XT=U ; Matches which are a perfect tie: 78 >= MAPQ >= 90, XT=R. Number of mismatches is not reflected in MAPQ but the information of total mismatches in both mates is found in the NM flag.
P-GEUV-6
nucleic acid sequencing protocol
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. 75 bp paired-end sequencing was done to the depth of a minimum of 20M mapped reads.
P-GEUV-5
nucleic acid library construction protocol
Sample processing for sequencing was done in a random order in each of the seven laboratories. Two batches of replicates were done: 5 samples were sequenced in every laboratory (twice in the University of Geneva), and additionally, 168 samples (mostly CEU and YRI samples) that were originally sequenced in the other laboratories were prepped and sequenced at about 1/2 of the normal coverage in University of Geneva. Library preparation was done with TruSeq RNA Sample Prep Kit v2 using the high-throughput protocol.