For the whole genome gene expression analysis, we used DirectHyb HumanHT-12, version 4.0 (Illumina, San Diego, CA, USA) according to the manufacturer's instructions, and the analysis was performed at the Swegene Center for Integrative Biology at Lund University.
For the whole genome gene expression analysis, DirectHyb HumanHT-12 v4.0 (Illumina, San Diego, CA) was used according to the manufacturer's instructions, and the analysis was performed at SCIBLU core facility at Lund University.
Subsequently, mRNA was isolated from total RNA using the Oligotex mRNA Mini Kit (Qiagen, Hilden, Germany) according to manufacturer's instructions, and the SSH analysis was conducted as previously described [ 21, 95] using the PCR-Select cDNA Subtraction Kit from Clontech (Mountain View, CA, USA), according to the manufacturer's protocol.
RNA samples were also tested for their quality using the RNA 6000 LabChip kit (Agilent Technologies) following the manufacturer's instructions, and RNA analysis was evaluated with the 2100 Bioanalyzer (Agilent Technologies).
No additional instructions regarding the analysis were provided.
MS-MLPA was performed according to the manufacturer's instructions, and data analysis was carried out with Coffalyser software v.8 (MRC-Holland).
RNA was isolated from occipital, parietal, and temporal cortices using the RNeasy mini kit (Qiagen, Gaithersburg, MD, USA) following the manufacturer's instructions and RNA analysis performed by Nanostring.
The sequencing was performed using the Ion PGM 200 Sequencing Kit according to the manufacturer's instructions (Life Technologies), and the data analysis was performed using CLC Genomics Workbench 5 modules.
Dead cells were identified using the LIVE-DEAD Fixable Violet Dead Cell Stain Kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions and excluded from the analysis.
After extraction with TRIzol (Invitrogen) following the manufacturer's instructions and agorose gel analysis, total RNA bands were visualized under UV light [30].
T/C-28a2 cell death was monitored by FITC-conjugated annexin V and PI double staining (V13242), performed according to the manufacturer's instructions, and analysis by flow cytometry (FACSCalibur flow cytometer (Becton Dickinson, San Jose, CA).
