Human genome u133a plus 2.0 array

The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138⁺ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody. To perform survival analysis, GSE2658 dataset of 559 MM patients and TCGA MM RNA sequencing dataset (MMRF-CoMMpass) of 787 cases with MM including clinicopathological information were downloaded from GEO database and TCGA (https://tcga-data.nci.nih.gov/) databases, respectively. For the retrospective cohort, the patients' characteristics were estimated by Pearson test χ² or Fisher's exact test, indicating no significant statistical difference.

The Gene Expression Omnibus database (GEO) is a public functional database for high- throughput screening of gene expression data, microarray data, and gene chips. In this study, we recovered genome expression datasets from GEO (Affymetrix Human Genome U133A Plus 2.0 Array, Affymetrix Human Genome U95A Array, and Affymetrix Human Genome U133 Plus 2.0 Array) [GSE1987, GSE17073, GSE 54495, GSE118370]. The GSE1987, GSE17073, GSE 54495, and GSE118370 datasets contain 28, two, 17, and six NSCLC tissue samples and 9, 10, 13, and six non-cancer tissue samples, respectively (Table 1). The software tools used in this study are listed in Supplementary Table 1.

In this study we analyzed 1 independent microarray dataset from ALS patients. Processed gene expression data were utilized with accession number GSE106382 [23 (link)] (Affymetrix Human Genome U133A Plus 2.0 Array) from NCBI’s Gene Expression Omnibus (GEO) database [24 (link)], which studied the molecular mechanisms of the fALS/sALS, and/or drug-treated ALS models based on their expression profiles. The GSE106382 dataset containing 24 samples from fALS patients with FUS, SOD1 or TDP43 mutations, and sALS versus healthy controls, was obtained from iPSC-derived MNs. From this large dataset, we analyzed a subset comprising 4 datasets each for FUS- and SOD1-ALS subtype (GSM2836938, GSM2836939, GSM2836942 and GSM2836943) compared to 4 healthy controls (GSM2836934, GSM2836935, GSM2836936, GSM2836937) that met the inclusion requirements respectively. For gene expression profiling assays, motor neuron populations in neuronal cell culture at approximately 40 days in vitro (DIV) were analyzed in both datasets. We processed and analyzed all the datasets and identified DEGs with p-values < 0.05 and log2 absolute values for fold control FC ≥ 1.5 (see below method).

Total RNA was isolated from HepG2.2.15 cells transfected with miR-449a and miR-con and subjected to microarray analysis using Affymetrix Human Genome U133A Plus 2.0 Array according to the manufacturer’s instructions. Differentially expressed genes were identified using Student’ t test on log-transformed data, and the results are represented as a heatmap using Spotfire (TIBCO Software Inc., Somerville, MA). These genes were further subjected to Gene Set Enrichment Analysis (GSEA) to identify the biological patterns of the genes. The significance threshold for the permutation test was set at P < 0.05.