2010
DOI: 10.1038/nature08903
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Transcriptome genetics using second generation sequencing in a Caucasian population

Abstract: Gene expression is an important phenotype that informs about genetic and environmental effects on cellular state. Many studies have previously identified genetic variants for gene expression phenotypes using custom and commercially available microarrays. Second generation sequencing technologies are now providing unprecedented access to the fine structure of the transcriptome. We have sequenced the mRNA fraction of the transcriptome in 60 extended HapMap individuals of European descent and have combined these … Show more

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Cited by 758 publications
(831 citation statements)
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References 33 publications
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“…77,78 Convincing evidence for allelic imbalance in CD6 gene was shown by RNA-Seq at a multiple sclerosis-associated SNP (rs17824933), confirming previous GWAS, and linking a polymorphism to CD6 gene expression changes. 79 Coupling RNA-Seq to other NGS applications (ChIP-Seq and exome sequencing), may reveal in the same sample different layers of complexity, showing the interplay among them (Figures 1 and 2).…”
Section: Rna-seq In Human Complex Diseases V Costa Et Alsupporting
confidence: 71%
“…77,78 Convincing evidence for allelic imbalance in CD6 gene was shown by RNA-Seq at a multiple sclerosis-associated SNP (rs17824933), confirming previous GWAS, and linking a polymorphism to CD6 gene expression changes. 79 Coupling RNA-Seq to other NGS applications (ChIP-Seq and exome sequencing), may reveal in the same sample different layers of complexity, showing the interplay among them (Figures 1 and 2).…”
Section: Rna-seq In Human Complex Diseases V Costa Et Alsupporting
confidence: 71%
“…We used the splice junction sensitive mapper Tophat 2.01.13 [32] with default settings, and mapped by applying the bowtie 2.2.4 [33] short read mapper. The counts per gene were estimated by using flux-capacitor [34]. To estimate differential expression, we used the R package Deseq2 [35] with a cutoff of log2fold change of 1.5.…”
Section: Methodsmentioning
confidence: 99%
“…Short sequence data produced for two RNA-seq studies 8,9 were obtained from GEO using accessions GSE19480 and GSE25030. The SRA (sequence read archives) files were downloaded and subsequently converted into FASTQ files using the NCBI SRA toolkit program, fastq-dump (v 2.1.16).…”
Section: Rna Sequencing Datamentioning
confidence: 99%
“…As a result, none of the large-scale RNA-seq studies in humans have been focused on characterizing mtDNA transcription. Comprehensive transcriptomic data sets from largescale RNA-seq studies have revealed significant expression variation for nuclear genes, 8,9 but to date virtually no progress has been made toward investigating expression variation in mtDNA genes. The lack of a precedent for evaluating the expression variability of mtDNA genes will ultimately hinder the understanding of mitochondrial biology as well as the advance of mitochondrial medicine.…”
mentioning
confidence: 99%
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