Clariom s microarray

Following the quantification of gene expression with the Clariom S microarray, raw .CEL files were uploaded into the Transcriptome Analysis Console v4.0.2 (TAC) (Thermo Scientific). The H. sapiens genome was used to generate the reference annotations. Two analyses ensued. First, pairwise comparisons were performed to determine mRNAs that were altered from PRE within each bout. A gene target was considered significant if gene expression exceeded a ±1.5-fold-change from PRE and the p-value was less than 0.01. Second, two-way repeated measures (2 × 2) ANOVAs, with the eBayes correction factor applied, were performed to detect genes that differed between bouts from PRE to 3 h POST and PRE to 6 h POST. For this statistical analysis, gene expression was considered significant if a fold-change over times between bouts of ±1.5 was exceeded and the interaction p-value was less than 0.01. Bioinformatics using gene lists from both analyses was performed using PANTHER v17.0 [43 (link),44 (link)]. All mRNA data can be accessed on Gene Expression Omnibus (URL: www.ncbi.nlm.nih.gov/geo/; GEO accession number: GSE220899 (uploaded on 14-12-2022 and will be made public on 1-6-2023)).

Microarray data from a previous study (unpublished) were analyzed and used to investigate the expression of Sur1-Trpm4 post-ICH. In that study, 10 animals (n = 5 per group) were randomly assigned to sham or collagenase ICH similar to our moderate stroke (~40 μL). At 24 hours after ICH, animals were euthanized and ipsilateral cortex (adjacent to the hematoma, peri-hematoma zone) as well as contralateral CA1 (a region previously shown to undergo cell compression after moderate to large bleeds) were dissected and flash frozen. RNA was extracted using a trizol-based extraction kit (Direct-zol, Zymo Research). Samples were analyzed with Clariom S microarray (Thermo Fisher Scientific) and data was analyzed using Partek (v7.0, St. Louis, MO). Here, we present the data for expression of Abcc8 (codes for Sur1) and Trpm4 in both regions.