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Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq

R. Kusko,J. Brothers,Gang Liu,Lingqi Luo,B. J. Guardela,J. Tedrow,Yuriy O Aleksyev,Ivana V. Yang,M. Correll,M. Geraci,John Quackenbush,F. Sciurba,M. Lenburg,D. Schwartz,J. Beane,N. Kaminski,A. Spira

Published 2012 in BMC Proceedings

ABSTRACT

Methods 87 LGRC lung tissue samples were sequenced on the Illumina GAIIx, generating 75 nt paired-end reads and approximately 30-40 million reads per sample. Using gapped aligner Tophat, an average of 85% of reads aligned to hg19. Gene expression was quantified using Cufflinks and Ensembl59 known gene annotation (n = 24,249 genes). All lung tissue samples used in this study, as well as additional LGRC lung tissue samples, were run on Agilent V2 human whole genome arrays and Agilent V3 human miRNA microarrays.

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