Humanht 12v4.0 expression beadchip arrays

Tissue samples were homogenized with a motorized pellet pestle, and total RNA was extracted using AllPrep DNA/RNA Micro kits (Qiagen). Samples were amplified (RiboAmp Plus 1.5-round RNA Amplification, Applied Biosystems) for the production of biotinylated cRNA (Bioarray High Yield RNA Labeling, ENZO) and subsequently hybridized to HumanHT-12v4.0 Expression BeadChip arrays (Illumina) that were scanned on a BeadStation system following manufacturer’s instructions. A total of 90 BeadChip arrays were used to generate gene expression profiles for dorsolateral, ventrolateral, and ventromedial prefrontal cortex from 18 females and 12 males. No pooling of samples across monkeys or regions was necessary. Prefrontal cortical regions, sex, and stress treatment conditions were randomly counterbalanced across separate BeadChip arrays.

The study was performed with two cohorts (GSE112676 and GSE112680) and gene expression evaluated using two microarray platforms (Illumina HumanHT-12 V3.0 and HumanHT-12 V4.0 expression beadchip arrays) [31 (link)]. The V3.0 platform was used to profile expression in the GSE112676 cohort (n = 233 ALS and 508 CTL samples), and the V4.0 platform was used to profile expression in the GSE112680 cohort (n = 164 ALS, 137 CTL and 75 MIM samples) (Additional file 2A). Cohort demographics have been described previously [31 (link)]. In brief, ALS, CTL and MIM groups each included a higher percentage of males (≥ 55.3%; Additional file 2B) with average ages of 63.6, 62.6 and 57.9, respectively (Additional file 2C). Most patients (> 60%) had spinal- rather than bulbar-onset ALS (Additional file 2D). The GSE112680 cohort had a larger percentage of patients with C9orf72 repeat expansions (12.8% vs. 5.2%, Additional file 2G). Survival was defined as the time interval between disease onset to death, tracheostomy or noninvasive ventilation [31 (link)]. Given this definition, median survival was 2.44 years with 50% of patients surviving 1.59 to 3.87 years (Additional file 2F). The 75 MIM patients had been diagnosed with diverse ALS-like conditions, but the most common diagnoses were benign fasciculations (n = 9), spinal muscular atrophy (n = 8) and myelopathy (n = 8) (Additional file 2G).