Experimental preparation of #RNAseq samples

This winter, the Master students preformed the experimental part of our RNA-seq. This blog is a bit late, so they have in the meantime started the bioinformatics analysis, which will be reported in a future blogpost (hopefully less late than this one).

So, four conditions to study gene expression:

growth conditions

Growth of bacteria in: liquid medium with succinate; liquid medium with toluene; sand with succinate; sand with toluene.

And after extraction the RNA looks good:

QC of RNA, 4 conditions with 4 replicates each

QC of RNA, 4 conditions with 4 replicates each

Quality control of the rRNA depletion process (Bioanalyzer report): no rRNA, no degradation.

Quality control of the rRNA depletion process (Bioanalyzer report): no rRNA, no degradation.

Quantification shows a very good yield.

bioanalyzer2

Quality Control (Bioanalyzer): near optimal size distribution; similar profiles for all samples.

So all these samples were sent to our Genomic Technologies Facility, and the single end reads found their way to our Vital-IT cluster.

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