Gene expression profile at single level of 8 cell lines isolated from IDH1-mutant diffuse glioma tumors

Diffuse low-grade gliomas are incurable brain tumours that often carry a mutation in the IDH1 gene. These tumours are heterogeneous and have different types of tumour cells. They can progress toward high grade gliomas. To understand the diversity of tumour cells and how they arise, we have performed single RNA seq of 8 cell lines derived from IDH1 mutant patients. Some cell lines maintained the IDH1 mutation while others lost it. We analysed these cultures when growth factors are present or absent for 4 days to promote differentiation. The 8 cell lines (LGG85, LGG275, LGG336, LGG349, BT138, BT237, BT54, BT88) were grown in neurospheres in DMEM/F12 media + N2 + B27 and EGF/FGF2/Heparin (GF= growth factor condition) or on poly-D-lysin/laminin without EGF/FGF2/Heparin (noGF= no growth factor condition). Ater 4 days, cells were dissociated and processed for scRNA seq analysis using 10X Chromium technology. The libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent kits V3.1 (Dual Index) from 10X Genomics. The clustering and sequencing steps were performed on an Illumina NovaSeq 6000 using the SBS (Sequence By Synthesis) technique with the NovaSeq Reagent Kits.