Hello,
We would like to perform a transcriptomic experiment in D. Melanogaster (control vs Knock down).
We are interested to identified in the differential transcript including small differences of expression (e.g: Transcription factor) but not specifically alternative splicing, SNPs, RNAi ...
The key elements of this study are to have an accuracy measure of differential expression of transcripts.
The question is what technique would be more appropriate to compare our comparaison control our vs condition "knockdown" (regardless of price).
Unfortunately I can’t find simple information in the literature between the comparison between microarrays (1 slide – 18K) and RNA-seq (40 million read in illumina).
We have the chose to use:
- 6 replicates (slides) in dye switch design
- 4 replicates/condition with 40 million of Reads in illumina
Could you give me some elements that will guide my choice
Thank you in advance for your answers
We would like to perform a transcriptomic experiment in D. Melanogaster (control vs Knock down).
We are interested to identified in the differential transcript including small differences of expression (e.g: Transcription factor) but not specifically alternative splicing, SNPs, RNAi ...
The key elements of this study are to have an accuracy measure of differential expression of transcripts.
The question is what technique would be more appropriate to compare our comparaison control our vs condition "knockdown" (regardless of price).
Unfortunately I can’t find simple information in the literature between the comparison between microarrays (1 slide – 18K) and RNA-seq (40 million read in illumina).
We have the chose to use:
- 6 replicates (slides) in dye switch design
- 4 replicates/condition with 40 million of Reads in illumina
Could you give me some elements that will guide my choice
Thank you in advance for your answers