What is the typical cost of carrying out a microarray experiment compared to a similar experiment using RNA-seq? For example: 10 human exon arrays versus RNA-seq for the same 10 individuals.
For microarray: cost of reagents, cost of 10 exon arrays; assume the chip scanner is present in the lab. For RNA-seq: cost of reagents, cost of sequencing at a commercial sequencing center.
I do not have any wet-lab experience so please advise how to better phrase this question.
Fabulous response. I now have good ball-park figures in mind. Thanks. ^-^ PK
This answer is now quite out of date with respect to RNAseq costs. These still vary widely depending on the protocol, target number of reads, etc. However to update the ballpark numbers I estimate that a typical RNA experiment starting from isolated RNA (including sample management, Illumina TruSeq Stranded library construction, and sequencing) might cost $600, $800, $1000 or $1400 per sample if multiplexing 8, 4, 3 or 2 samples per lane on a HiSeq2500/HiSeq4000, with 2x100(or 125)bp reads for a modest sized project (~20 samples). Costs will be slightly lower on a HiSeq4000 and will likely go lower yet once HiSeqX is released for RNAseq. NOTES: Remember these are rough estimates. Your local core may (likely) charge a little more. Some genome centers may also be able to do better for larger projects. These prices don't include any indirect costs that may come into play. The amount of multiplexing you plan for will depend on the analysis/experimental goals of the project. Adding an exome capture step may allow increased multiplexing, again depending on your experimental goals.