Public RNA-Seq and Microarray samples from same tissue

Question

[Ar]

I am looking for a public dataset that has RNA-Seq and Microarray samples from the same tissue &/ same conditions but I am interested in the RNA-Seq dataset that has batch effects. Can you please share the GEO id or Array Express link ?Thanks!

Answer 1

[Kevin Blighe]

Researchers will not typically study batch effects directly if they have another end-point of interest, and may only make a loose reference to batch in supplementary methods. As such, it may be difficult to find the exact experimental set-up that you want.

However, you should be aware that the TCGA has expression data on various cancers as both RNA-seq and cDNA microarray, and, because it's the TCGA, most of these samples will overlap centers and therefore be from different batches. Take a look at the NCI's Genomic Data Commons to see what you can find.

Also take a look at these:

• Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
• Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells