Which sequencing platform would be best for the transcriptome?

Hello,

Do you know if is that possible to identify bacterial enzymes (from microbiota) by analyzing transcriptomics data from a human tissue (i.e. TCGA samples)?

Thanks for you response!

Consider samples from tissues A and B of a species X collected from geographical location 1 and samples from the same tissues A and B collected from geographical location 2. If we are to do differential expression analysis for all the samples, what will be the best way to generate reference transcriptome assembly? Pooling in reads from all samples together to do one transcriptome assembly OR performing assemblies for each sample separately and then pooling in the non-redundant assembled transcripts? Any other precautionary measures to be taken for such an analysis? Please share references if possible.

Can anyone recommend a good mouse transcriptome database that is organized based on tissue? I am looking to find a list of protein coding mRNAs detected in whole blood.

Does anybody have an experience with stabilizing plant leaf tissues with RNAlater™-ICE Frozen Tissue Transition Solution? Is it necessary to homogenize the plant tissue for RNA isolation before using this solution?

We are going to use custom TaqMan TM Advanced miRNA Assays for microRNA quantification experiments in plants. These assays are not compatible with the use of U6 snRNA as a reference internal sRNA. Therefore, we are seeking suggestions on miRNAs that have been proved to be stable in plant leaf tissues under biotic stress conditions. Any experiences or any ideas? Many thanks in advance for your support.

Fabrizio

I'm thinking 2 hours. This is my first qPCR experiment on plants and I'm hoping to catch the earliest changes in root gene expression when iron is applied to leaf tissue.

I've found a similar study which considers "1 day later" after foliar application of iron. Gene expression in the roots must occur before that however. Do you think 2 hours is too short?

If 2 hours is not long enough to effect root gene expression, this would be a surprise to me and I would consider this an interesting result anyway! Gene expression in leaf tissue should be effected immediately after iron application, these will be subjected to qPCR as well...

Any comments are appreciated, I anticipate treating/processing plants soon. Such a tense and anxious time, wish me luck :)

For example, if I have 1 million cells in suspension and from this suspension I separate single cells, how many cells should be sequenced individually to have a statistically significant result?