Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

Chapter 6
Digital Transcriptome Profiling
Contents
6.1 Clinical Data . . . . . . . . . . . . . . . . . . . . . . . . . . 120
6.2 Tag mapping . . . . . . . . . . . . . . . . . . . . . . . . . . 121
6.3 Copy Number Aberrations . . . . . . . . . . . . . . . . . . 125
6.4 Core Differentially Expressed Genes . . . . . . . . . . . . . 129
6.5 Large-scale qRT-PCR Validation . . . . . . . . . . . . . . . 136
6.6 Literature Mining for Differentially Expressed Genes . . . . 142
6.7 Isoform Differential Expression . . . . . . . . . . . . . . . . 144
6.8 Long ncRNA Differential Expression . . . . . . . . . . . . . 157
6.1 Clinical Data
The clinical data available for our cell lines are somewhat limited due to pa-
tient consent forms prohibiting surgeons from revealing it. However, we do
know that all of our GNS cell lines are clinically classified as primary glioblas-
tomas, not secondary. Consistent with this, the PCR experiments performed
by Steven Pollard on our GNS cell lines to establish the presence or absence
of IDH1 and IDH2 mutations found no evidence of any mutation in their re-
spective loci (oral communication). In the paper by Pollard et al [404] the
genetics of our GNS cell lines are described using SNP6.0 arrays, which iden-
tified "classic" mutations, in particular frequent loss of CDKN2A:ARF, gains
of CDK4 and general glioblastoma-pertinent gene instability. The age of the
patients is described in the paper and summarised in table 6.1 below.
120