Gene expression profiling of human glioblastoma cells WT and KO for JAM3
Description
This dataset contains transcriptomic data from the comparison of wild-type (WT) and JAMC^-/- GSC1 clones, as presented in Figure 3 of the associated study. Four independent biological samples were analyzed using 3′ RNA sequencing to assess differential gene expression between these two conditions. The experiment was conducted to explore the transcriptional changes associated with the knockout of the JAMC gene in glioblastoma stem-like cells.
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Steps to reproduce
For the comparison of WT and JAMC-/- GSC1 clones presented in Figure 3, four independent samples were prepared and RNA content was analyzed by 3’ Sequencing RNA Profiling at the Genomics and Bioinformatics Core Facility (GenoBiRD, Biogenouest, IFB, Nantes). Briefly, total RNA was isolated using the RNeasy Mini Kit (Qiagen) and clean samples (DO260/280 and 260/230>1.8) were submitted for quality control on a Bioanalyzer Tape Station (Agilent). RNA libraries were prepared (Ambion) and transcriptome analysis was carried out (Affymetrix, eBioscience, for co-culture and HiSeq 2500, Illumina, for clones). Data were demultiplexed and analyzed with Illumina Bcl2fastQ2 software. Reads were aligned against human reference transcriptome (hg19) and differential analysis was performed with the DESeq2 tool.