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Table 1 Previous studies comparing microarray and sequencing platforms for the measurement of gene expression

From: A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat

Study Array platform Sequencing platform Species Tissue/cell line Replication Experimental intervention/design
Marioni et al. 2008 [20] Affymetrix HG-U133 Plus 2.0 Illumina Genome Analyzer Human Liver/kidney Technical replications (3 per tissue for microarray, 7 different flow cell lanes for RNA-seq). All RNA was taken from a single human male. Aliquots from each sample were then used for RNA-sequencing and microarray analysis.
Bradford et al. 2010 [21] Affymetrix Human Exon 1.0 ST Applied Biosystems SOLiD v3 platform Human MCF-7 and MCF-10a breast cancer lines Technical replication (2 x MCF-7, 1 x MCF-10). Samples hybridised in triplicate to microarrays. RNA analysed on the SOLiD platform and the same RNA samples hybridised in triplicate to Affymetrix Exon 1.0ST arrays.
Bottomly et al. 2011 [22] Affymetrix MOE 430 2.0 and Illumina MouseRef-8 v2.0 Illumina GA IIx Mouse Striatum Biological replication, independent groups used for different technologies. B6 strain mice were compared to D2 strain. For RNA-seq, 10 B6 and 11 D2 were used; for Affymetrix arrays 7 D2, 10 B6; for Illumina arrays 12 D2 12 B6. A subset of this group of mice were also used for RNA-seq.
Toung et al. 2011 [23] Affymetrix HG Focus Array Illumina 1G Genome Analyzer Human B-cells Biological replicates (20 unrelated individuals). Independent samples (from same individuals) were used for different technologies. B-cell lines were taken for 20 different individuals (10 male, 10 female). Cells were grown and total RNA extracted.
Su et al. 2011 [24] Affymetrix Rat Genome 230 2.0 Illumina GA II Rat Kidney Biological replication (4 rats per condition). Eight rats in total, 4 were administered with aristolochic acid, 4 with control vehicle. RNA was extracted from kidneys of each rat; each RNA sample was assayed using RNA-seq and miroarrays
Fu et al. 2009 [25] Affymetrix Human Exon 1.0 ST Illumina Solexa Sequencer (precise model name not given) Human Brain Biological replication (two groups of 5 pooled individuals). Two independent samples were used, each containing pooled mRNA from 5 adult human individuals. These samples were used as input for RNA-seq, microarray and proteomic analysis.
Griffith et al. 2010 [26] Affymetrix Human Exon 1.0 ST and Nimblegen custom array Illumina GA II Human Colorectal cancer cell-lines One sample per condition. 5-fluorouracil resistant cell lines compared to non-resistant lines. The same input was used for microarrays and RNA-seq.
Bullard et al. 2010 [27] Affymetrix U133 Plus 2.0 Illumina GA II Human Brain reference DNA and universal human reference DNA Technical replication. Various experimental designs were employed in order to teaste apart the effects of flow cell and library preparation on the results.
Kogenaru et al. 2012 [28] Agilent custom array Illumina GA IIx Xanthomonas citri subsp . citri . Whole organism Biological replication (3 replicates per strain). Comparison was made between wild-type and hrpX mutant strains. Biological replicates of each strain were grown in culture and the RNA was extracted.
Sîrbu et al. 2012 [29] Affymetrix and dual-channel microarrays Illumina GA II Drosophila Embryo development (time-series) Technical replicates were used for RNA-seq, biological replicates were used for microarray. Datasets were analysed and compared in terms of “reference” genes, which were highly likely to be expressed during embryogenesis. Several other technical measurements were also taken, including clustering and differential expression measurements.
Sekhon et al. 2013 [30] NimbleGen custom array Illumina GA II Maize 18 selected tissues representing 5 organs Biological replicates, compared to historical dataset. Samples were assayed by both technologies, and compared in terms of expressed genes and correlation.
Mooney et al. 2013 [31] Affymetrix Canine Genome 2.0 Illumina Hiseq 2000 Dog B-cell lymphoma Biological replication; same samples used for both technologies (10 case, 4 control samples). Investigation into the difference between technologies in terms of technical biases and pathways found.
Malone and Oliver 2011 [32] Nimblegen custom array Ilumina GA I Drosophila pseudoobscura Head Biological replicates (four for microarray; one of these replicates used for RNA-seq). RNA from males was compared to RNA from females. Four distinct RNA libraries were produced, with each library produced using 500–600 individual fly heads.