The transcriptome is not the proteome. So you look at quite different things. Microarrays give you a quite complete picture of the transcriptome as a whole, allowing you to investigate regulatory transcription networks. Given the array experiments and the data analysis is done "state of the art", array results are very reliable. But, to repeat myself: they are about the transcriptome, not about the proteome.
I would suggest that you do RNA-seq analysis and also try to examine miRNAs, circular RNAs, ncRNA, etc.role in implantation. This will give you a better 360 degree view of gene expression and after you analyze your data, you may like to corroborate your results with RT-PCR of differentially expressed genes....In addition, whole RNA kinetics will be clear and you may find, for example, micro RNAs having sophisticated control of gene expression during implantation......I am assuming that you are not interested in pursuing proteomic analyses at this stage of your work?
@Jochen, many thanks for response. Yes I am aware I am not looking at Proteome. Actually I realised I haven't framed question rightly. I was checking if Proteomic studies should be carried out at this stage itself as we eventually aim to study the microenviornment during the spatially restricted WOI. We have done microscopic and cellular assays including those on biopsies. We are starting with microarray for now. But your answer helped to crystallise the path.
@Kulvinder, excellent suggestion and we did try to seek that path initially. We have done RT PCR studies of few genes and have some encouraging results. Two factors contributed to our decision in favour of Microarray. First we are looking at well annotated genes and RNA-Seq is both very expensive and mostly several experts opined as not yet matured in terms of data analysis. The interpretations are very important and require great deal of expertise. Seating in India, we had to reevaluate our strategy and we opted for Microarray. yes you are right about your last question. I already expressed it in my answer here. Much thanks for your response.
- Badges
- Science topic
- Similar topics
- Chemistry
- General Biochemistry
- Proteomics