Transcriptome Analysis of Sickle Cell Disease

Message RNA was purified from PBMCs, labeled and hybridized to Affymetrix Exon 1.0 ST Array for 35 patients of Howard cohort (Zhang et al. 2014a (link)), and to Affymetrix Gene 2.0 ST Array for 134 SCD patients selected from UIC cohort. Probe sequences were aligned to human genome assembly GRCh37 to select for probes with unique perfect alignment. Probes that interrogate multiple gene transcripts and that contain SNPs with ≥1% minor allele frequency in dbSNP dataset were removed. Probe intensities were log₂ transformed, background corrected and quantile normalized. Probe intensity was subtracted by the corresponding probe mean across samples. Gene expression level was summarized as mean intensity across probes within gene, using Gencode version 19. Batch effects of RNA labeling and array hybridization were adjusted using an empirical Bayes method (Johnson et al. 2007 (link)).

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Zhang X., Zhang W., Saraf S.L., Nouraie M., Han J., Gowhari M., Hassan J., Miasnikova G., Sergueeva A., Nekhai S., Kittles R., Machado R.F., Garcia J.G., Gladwin M.T., Steinberg M.H., Sebastiani P., McClain D.A, & Gordeuk V.R. (2015). Genetic polymorphism of APOB is associated with diabetes mellitus in sickle cell disease. Human genetics, 134(8), 895-904.

Publication 2015

Exon 1.0 ST Array Gene 2.0 ST Array

Exon Gene Gene expression Human genome Hybridization Multiple gene Patients Snps

Corresponding Organization : University of Illinois at Chicago

Other organizations : Northwestern University, Howard University, Chuvash State University, University of Arizona, University of Pittsburgh, Boston University, Wake Forest University

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Variable analysis

independent variables

RNA labeling
Array hybridization

dependent variables

Gene expression level

control variables

Probe sequences that have unique perfect alignment to the human genome
Probes that interrogate multiple gene transcripts and contain SNPs with ≥1% minor allele frequency in dbSNP dataset were removed
Batch effects of RNA labeling and array hybridization were adjusted using an empirical Bayes method

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