Integrative Genomics Study of EBV Lymphoblastoids

Total RNA was extracted from EBV transformed lymphoblastoid cell line pellets by the TRIzol reagent (Ambion), and mRNA and small RNA sequencing of 465 unique individuals was performed on the Illumina HiSeq2000 platform, with paired-end 75bp mRNA-seq and single-end 36bp small RNA-seq. Five samples were sequenced in replicate in each of the seven sequencing laboratories. The mRNA and small RNA reads were mapped with GEM³¹ and miraligner^{32 (link)}, respectively, with an average of 48.9M mRNA-seq reads and 1.2M miRNA reads per sample after QC. Numerous transcript features were quantified using Gencode v12^{33 (link)} and miRBase v18^{34 (link)} annotations: protein-coding and lincRNA genes (16,084 detected in >50% of samples), transcripts (67,603; with FluxCapacitor^{7 (link)}), exons (146,498), annotated splice junctions (129,805; analyzed in detail in Ferreira et al. submitted), transcribed repetitive elements (47,409), and mature miRNAs (715). Data quality was assessed by sample correlations and read and gene count distributions, and technical variation was removed by PEER normalization^{35 (link)} for the QTL and miRNA-mRNA correlation analyses^{11 (link)}. The samples clustered uniformly both before and after normalization. The genotype data was obtained from 1000 Genomes Phase 1 data set for 421 samples (80× average exome and 5× whole genome read depth), and the remaining 41 samples were imputed from Omni 2.5M SNP array data. Furthermore, we did functional reannotation for all the 1000 Genomes variants using Gencode v12. QTL mapping was done with linear regression, using genetic variants with >5% frequency in 1MB window and normalized quantifications transformed to standard normal. Permutations were used to adjust FDR to 5%. Full details are provided in Supplementary Methods.

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Lappalainen T., Sammeth M., Friedländer M.R., ‘t Hoen P.A., Monlong J., Rivas M.A., Gonzàlez-Porta M., Kurbatova N., Griebel T., Ferreira P.G., Barann M., Wieland T., Greger L., van Iterson M., Almlöf J., Ribeca P., Pulyakhina I., Esser D., Giger T., Tikhonov A., Sultan M., Bertier G., MacArthur D.G., Lek M., Lizano E., Buermans H.P., Padioleau I., Schwarzmayr T., Karlberg O., Ongen H., Kilpinen H., Beltran S., Gut M., Kahlem K., Amstislavskiy V., Stegle O., Pirinen M., Montgomery S.B., Donnelly P., McCarthy M.I., Flicek P., Strom T.M., Lehrach H., Schreiber S., Sudbrak R., Carracedo Á., Antonarakis S.E., Häsler R., Syvänen A.C., van Ommen G.J., Brazma A., Meitinger T., Rosenstiel P., Guigó R., Gut I.G., Estivill X, & Dermitzakis E.T. (2013). Transcriptome and genome sequencing uncovers functional variation in humans. Nature, 501(7468), 506-511.

Publication 2013

Exome Exons Gene Genetic variants Genomes Genotype Lincrna Mirna Mrna Pellets Protein Repetitive elements Replicate Rna seq Transformed cell line Trizol

Corresponding Organization : University of Geneva

Other organizations : Centro Nacional de Análisis Genómico, Centre for Genomic Regulation, Leiden University Medical Center, University of Oxford, Wellcome Centre for Human Genetics, European Bioinformatics Institute, Wellcome Trust, Kiel University, Helmholtz Zentrum München, Uppsala University, Science for Life Laboratory, Max Planck Institute for Molecular Genetics, Massachusetts General Hospital, SIB Swiss Institute of Bioinformatics, Fundación Pública Galega de Medicina Xenómica, Servicio Gallego de Salud, Universidade de Santiago de Compostela, Hospital Del Mar, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública

Top 5 similar protocols

Protocol cited in 486 other protocols

Variable analysis

independent variables

Genetic variants with >5% frequency in 1MB window

dependent variables

Normalized quantifications of protein-coding and lincRNA genes (16,084 detected in >50% of samples), transcripts (67,603), exons (146,498), annotated splice junctions (129,805), transcribed repetitive elements (47,409), and mature miRNAs (715)

control variables

Technical variation was removed by PEER normalization
Five samples were sequenced in replicate in each of the seven sequencing laboratories

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!