Journal: BMC Research Notes

Article Title: Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success

doi: 10.1186/s13104-016-2209-x

Figure Lengend Snippet: Flow diagram showing the number of SNPs remaining after each step of the SNP detection pipeline for both an Illumina Infinium iSelect HD array ( blue circles ) and an Affymetrix Axiom array ( purple circles )

Article Snippet: Blasting the Infinium and Affymetrix SNP sequences with an e-value threshold of 1e −12 recovered 24,247 and 22,368 hits respectively.

Techniques:

Journal: PLoS ONE

Article Title: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

doi: 10.1371/journal.pone.0025279

Figure Lengend Snippet: ( A ) Comparison of estimated log 2 -fold changes from analysis of microarrays (x-axis) and RNA-Seq using GENE-counter running NBPSeq (y-axis). Only induced genes measurable by both platforms are presented. Differentially induced genes are colored to highlight genes uniquely identified using microarrays (open red down triangles) or RNA-Seq (open blue up triangles) and found common between the two methods (purple crosses). ( B ) Three-way Venn comparing differentially expressed genes identified from GENE-counter's assessment of RNA-Seq data and analysis of microarrays. Only genes measurable using both methods were included in the comparison.

Article Snippet: The mRNA labeling, hybridization, and scanning of Affymetrix ATH1 microarrays were done by the CGRB core facility at OSU.

Techniques: Comparison, RNA Sequencing