Performing transcript-specific QC of an RNAseq library

[bpinder]

Hello

I want to perform RNAseq on a low input sample. I would like to do RT-qPCR to verify that my samples are behaving as expected but unfortunately I will be using up almost all of my total RNA to generate a library (I have 110ng in my lowest sample input).

Is it possible to take some of the library and use it to do qPCR for my transcripts of interest?

Thank you
Ben

[bpinder]

Follow-up question (help appreciated)

I will be getting some of my RNA-seq cDNA library which is being made with an Illumina Truseq preparation kit. I would like to perform real-time PCR.
In the past I have assayed these transcripts using SYBR chemistry but am concerned that this will not work because of the nature of the fragmented library.
Does anyone have experience with this? Do I need to switch to TaqMan probes?
Thank you,
Ben