Human genome u133 plus 2.0 array

Four datasets of the mRNA expression profiles of the whole blood, blood lymphocytes, or peripheral blood mononuclear cells (PBMC) of schizophrenia patients and their corresponding healthy controls were downloaded from the NCBI’s GEO,¹ including GSE18312 [GPL5175, Affymetrix Human Exon 1.0 ST Array], GSE165604 [GPL16791, Illumina HiSeq 2,500 (Homo sapiens)], GSE27383 [GPL570, Affymetrix Human Genome U133 Plus 2.0 Array], and GSE38484 [GPL6947, Illumina HumanHT-12 V3.0 expression beadchip]. The information of each dataset is demonstrated in Table 1.
The four datasets contain a total of 309 samples, including 158 samples of schizophrenia patients and 151 samples of healthy controls (Table 1). The batch effects of these datasets were adjusted using the COMBAT function from the R package inSilicoMerging (Taminau et al., 2012 (link)). Then, a normalized merged expression matrix of the four datasets were generated and visualized by a box line plot. All these analyses were performed in the SangerBox platform.²

We complemented the staining-based analysis of the CD27 protein by detailed characterization of the expression profile on the mRNA level. The GENEVESTIGATOR platform (NEBION AG, Zurich, Switzerland) [55 ]), which integrates publicly available and manually curated microarray and RNA sequencing data sets, was used to extract the expression pattern of CD27 across various cell types. The integrative analysis algorithm was described by us in detail previously [53 (link),56 (link),57 ]. A selection of healthy human samples was made for the Affymetrix Human Genome U133 Plus 2.0 Array compendium and likewise for the Illumina mRNA-Seq (ref. Ensembl 75) compendium. The analysis was performed on each platform separately. The top 15 outcomes (ranked by the gene expression levels) were exported. Furthermore, the mRNA expression levels of CD27, ICOS, CXCR5, PDCD1, and CD3E were assessed in TFH cells using the above mRNA-Seq compendium.

Four microarray datasets including 587 BCa patients with clinical annotations and CSS information were downloaded from Gene Expression Omnibus (GEO). GSE13507 was produced by Illumina human-6 v2.0 expression beadchip and was used as the training set in our study. GSE31684 (Affymetrix Human Genome U133 Plus 2.0 Array) and GSE32894 and GSE32548 (Illumina HumanHT-12 V3.0 expression beadchip) were used as independent validation cohorts. Probe IDs were mapped to gene symbols according to the corresponding annotation file, and expression measurements of all probes linking to a same gene were averaged to obtain a single value. RSEM-normalized RNA-seq data, copy number data, and clinical phenotypes of MIBC samples were obtained from The Cancer Genome Atlas (TCGA). Copy number data and TPM data of 22 bladder cell lines were obtained from Cancer Cell Line Encyclopedia (CCLE) [9 (link)]. RMA normalized microarray expression data and IC50 values of different drugs for 1018 cell lines were accessed from Genomics of Drug Sensitivity in Cancer (GDSC) [10 (link)]. All microarrays and RNA-seq data included in this study were normalized and log2 transformed.

The gene expression datasets re-analyzed in this study were obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). We selected two gene expression profiles (GSE63067, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63067, PMID: 25993042 and GSE89632, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89632, PMID: 25581263) related to Homo sapiens’ NAFLD from the database. Among them, GSE63067 was based on the Agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), and GSE89632 was based on platform GPL14951 (Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip). GSE63067 (13 (link)) included 18 participants (2 SS, 9 NASH, 7 HC). Liver samples were obtained during laparoscopic bariatric surgery (for NAFLD) or laparoscopic cholecystectomy (for HC). GSE89632 (12 (link)) included 63 participants (20 SS, 19 NASH, 24 HC), and liver tissues were collected during percutaneous needle biopsy (for NAFLD) or as a wedge biopsy during hepatectomy (for HC). All of the data were freely available online.

The Gene Expression Omnibus (GEO) database collects and shares publicly a range of different high-throughput sequencing and microarray-based data sets. In our research, we searched the data sets, which consisted of patients with AMI and healthy controls. The microarray expression data sets (GSE48060, GSE60993, and GSE66360) were obtained and downloaded from the GEO database¹, including GSE48060 contributed by Suresh et al., GSE66360 contributed by Kramer et al., and GSE60993 contributed by Eun et al. (11 (link)–13 (link)). These data sets were based on GPL570 platform of Affymetrix Human Genome U133 Plus 2.0 array and GPL6884 platform of Illumina HumanWG-6 v3.0 expression beadchip, respectively. These three data sets were merged into a metadata, which was used as the training group. Moreover, GSE61144 contributed by Eun et al. was served as an external validation data set (13 (link)). The detailed information about our data sets and the annotation platform is listed in Table 1.

Four gene expression profiles (GSE9899, GSE27651, GSE12172, and GSE57477) were downloaded from the Gene expression omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo). GSE9899 included 18 ovarian LMP tumors and 267 EOC samples, GSE27651 included 8 LMP tumors and 22 EOC samples, GSE12172 comprised 30 LMP tumors and 60 EOC samples, and GSE57477 included 6 LMP tumors and 46 serous ovarian adenocarcinomas. The gene expression data of GSE9899, GSE27651 and GSE12172 were download from the platform of GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array), whereas GSE57477’ gene expression data was download from the platform of GPL10558 (Illumina HumanHT-12 V4.0 expression beadchip).