Hi all,
I would like to study the gene expression levels of 22 genes in 1200 different samples.
Since normal qPCR is humanly not doable here (26400 reactions) I would like to know if anyone knows of a high throughput plateform that would allow us to study a loooot of samples on only a few genes...
I have heard of Microfluidic plateforms. Anyone with experience on a few of these? Would that fit our experiments and what are the average costs of such an approach?
Thank you!
Nanostring might be another option.
http://www.nanostring.com/applications/technology
http://www.nanostring.com/media/pdf/LBL-10183-01_nCounter_Brochure.pdf
Fluidigm Biomark HD might also be an alternative for high-throughput qPCR.
https://www.fluidigm.com/products/biomark-hd-system
Hello Celine, As you look for the best high throughput qPCR platform to meet your needs, please also consider the SmartChip platform (http://www.wafergen.com/products/smartchip-real-time-pcr) from Wafergen BioSystems. The study you described in your question could be run on just 6 chips and would take less than two days to run on the SmartChip platform. You will also find that it offers great flexibility, throughput, costs per sample.
I would personally use deep sequencing, for example the custom targeted RNA sequencing library prep kit from illumina.
http://www.illumina.com/products/truseq-targeted-rna-expression-kits.html
You can multiplex up to 384 samples in a single Miseq run. It is usually more expensive than arrays or qRT-PCR, but given the sample number, prices should be competitive. Plus it is streamlined for high multiplexing and provides directly readcounts for easy analysis.
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