I have identified by RNA-seq a set of genes which I want to study in more detail using three different cell lines and conditions. This would be about 100 genes or I could expand to 1500. Which would be better...PCR array OR a dedicated microarray ( I could run many conditions in one slide) or there´s a NGS aproach for this that is cost-effective?
The RNA-seq approach would be the best, but its cost really depends of the genome size of your organism. The advantage of the RNA-seq approach is that you could study more than the 100 targeted genes, and maybe discover other interesting genes. However, depending on the number of conditions you are studying, this method can require time-consuming analyzes if you don't have a dedicated bioinformatician or standardized RNA-seq pipelines.
If you are only interested in your set of 100 genes (which requires that this set has been particularly well identified) or if your organism encompass a large genome, maybe you should consider making your own micro-array. It will be especially efficient if you have a lot of samples or conditions to analyze. However, you will lack the exhaustiveness of the RNA-seq approach.
But all-in-all, it really depends of your budget.
For an NGS approach you could use the QIAseq targeted RNA panels there are several pre-made panels which may suit your needs, or they also offer custom panels to cover all of the genes you require. These panels are limited to your gene selection and so will not be as all encompassing as untargeted RNAseq, however the use of molecular barcodes allows easy and reliable quantification of transcript levels.
This is probably the most cost-effective NGS approach for your requirements and is available for both Illumina and Thermo-Fisher instruments. It is also a multiplex system which allows for up to 96 unique samples on a single run. We have used this approach for a couple of projects and it is pretty straight forward, Qiagen also provide access to a specific analysis pipeline for analysis of the results.
https://www.qiagen.com/us/shop/sample-technologies/rna/qiaseq-targeted-rna-panels/#orderinginformation
https://www.qiagen.com/gb/shop/genes-and-pathways/custom-products/custom-array-products/qiaseq-targeted-rna-panels/
Hi
Since your targets are well identified, take a look at NanoString that offers a quantification solution for up to 700 targets with an easy analysis software.
fred
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