Open Access Highly Accessed Research article

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease

Nalini Raghavachari1*, Jennifer Barb2, Yanqin Yang1, Poching Liu1, Kimberly Woodhouse1, Daniel Levy45, Christopher J O‘Donnell46, Peter J Munson2 and Gregory J Kato3

Author Affiliations

1 Genomics Core Facility, Genetics and Development Biology, NHLBI, The National Institutes of Health, 10 Center Drive, Bldg 10, 8C 103B, Bethesda, 20892, USA

2 Mathematical and Statistical computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA

3 Hematology Branch, National Institutes of Health, Bethesda, MD, USA

4 The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA

5 The Center for Population Studies and the Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA

6 The Center for Cardiovascular Genomics and the Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA

For all author emails, please log on.

BMC Medical Genomics 2012, 5:28  doi:10.1186/1755-8794-5-28

Published: 29 June 2012

Additional files

Additional file 1 :

Figure S1. Gene Ontology analysis on the differentially expressed genes. The top 13 highly significant classification/functions of genes are shown in the figure.

Format: PPT Size: 137KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 2 :

Figure S2. Effect of Globin Reduction on RNA-seq expression. Y-axis: Read counts per transcript, normalized by median for globin reduced sample; X-axis: Read counts normalized by median for same sample using standard preparation. Correlation coefficient is 0.93.

Format: PPT Size: 128KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 3 :

Table S2. Validation of few differentially expressed genes by QPCR.

Format: XLS Size: 19KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4 :

Figure S3. Putative Exon 4A . UCSC Genome Browser view of the BAM files for each sample showing genomic region chromosome X: 55067500–5506725. The first 3 aligned tracks show the control samples, the following 5 tracks show the sickle cell disease samples. Aligned reads are Red if to the negative strands and blue if to the positive strands. The total reads per sample is: C3: 15,715,705, C4: 15,131,360, C5: 15,730,372, S6: 16,570,843, S1: 13,481,528, S2: 16,707,788, S3: 14,650,161, S4: 18,580,778 and S5: 16,460,443. S6: 16570843, S1.

Format: PPT Size: 166KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 5 :

Table S1. Complete List of differentially expressed genes (n = 331).

Format: XLS Size: 80KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data