Dear all,
We have developed a model on autism using zebrafish. Keeping this model in mind we are looking forward to explore the probable pathways involved in model. As per the literature I found that microarray or transcriptome analysis can be a good approach, but still confused to finalise one. I have been communicating with different companies for the same purpose among which one of the company person suggested to go for transcriptome analysis as it is in trend and can explore even unknown genes, on the other hand another company suggest to go for microarray and then transcriptome for specific pathways. They also suggested that proceeding directly for transcriptome will confuse us with data. As I am new to the feild I am bit confused that what would be a better approach and seeking help of experts on the same. Also I would like to know about the minimum samples to get valid and data
Any suggestions over the same will be helpful
Thank you
Shubham
Kindly refer the link below
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078644
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894192/
Regards
RNA-seq (transcriptome analysis) is the way to go; unfortunately, it does produce large datasets that can be a little troublesome for newcomers.
Dear Shubham,
I strongly suggest you to perform transcriptome analysis through RNA-Seq. Although microarrays would be definitely cheaper, maybe allowing you to analyse more replicates, RNA-Seq overcomes many issues deriving from microarrays. First, you're right, through RNA-Seq you will be able to detect and quantify both annotated and unannotated (as well as unknown intergenic expressed regions) transcripts, alternative splicing isoforms, long non-coding RNAs and so on. Through the microarrays you'd be able to simply quantify the annotated transcripts. Moreover, you will overcome the problem of the saturation for the extremely highly expressed transcripts and you will have a direct measure of the gene expression, not an indirect (flurescence based) quantification. Sincerely, I've never worked on zebrafish but for the complex genomes (i.e. mammalian) microarrays suffer also of cross-hybridation dued to the high amount of repetitive sequences. For all these reasons (and for many other that I cannot report here) I suggest you to go for transcriptome analysis.
Good luck!
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