GSE22035 (11 (link)), GSE3744 (12 (link)), GSE5764 (13 (link)), GSE21422 (14 (link)) and GSE26910 (15 (link)) profile datasets were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/ ) and based on a GeneChip Human Genome U133 Plus 2.0 Array platform (Affymetrix; Thermo Fisher Scientific, Inc., Waltham, MA, USA). The datasets contained 151 tissue samples, including 88 invasive ductal carcinoma tissues, 23 invasive lobular carcinoma tissues, five ductal carcinoma in situ tissues and 38 adjacent non-tumorous tissues.
Genechip human genome u133 plus 2.0 array platform
Manufactured by Thermo Fisher Scientific
Sourced in United States
The GeneChip Human Genome U133 Plus 2.0 Array is a gene expression microarray platform developed by Thermo Fisher Scientific. The array contains probes designed to measure the expression levels of over 47,000 transcripts and variants, representing approximately 38,500 well-characterized human genes.
Automatically generated - may contain errors
Lab products found in correlation
Rnalater, by Thermo Fisher Scientific (2 mentions)
Genespring gx 12, by Agilent Technologies (1 mentions)
Platinum taq dna polymerase, by Thermo Fisher Scientific (1 mentions)
Hybridization oven 645, by Thermo Fisher Scientific (1 mentions)
Fluidics station 450, by Thermo Fisher Scientific (1 mentions)
Genechip scanner 3000, by Thermo Fisher Scientific (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Nexus expression 3, by BioDiscovery (1 mentions)
Human lncrna microarray v4.0 platform, by Arraystar (1 mentions)
11 protocols using genechip human genome u133 plus 2.0 array platform
1
Breast Cancer Transcriptome Profiling
2
Microdissection and Transcriptomic Analysis of Human Kidney
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By searching in GEO database (http://www.ncbi.nlm.nih.gov/geo/ ), GSE104948, GSE104954, GSE108109, GSE108112 and GSE108113 profile datasets which met our requirements were downloaded. The datasets of GSE104948 and GSE104954 were based on a GeneChip Human Genome U133 Plus 2.0 Array platform (Affymetrix; Thermo Fisher Scientific, Inc., Waltham, MA), and datasets of GSE108109, GSE108112, and GSE108113 were based on a GeneChip Human Gene 2.1 ST Array platform (Affymetrix; Thermo Fisher Scientific, Inc., Waltham, MA). The samples of GSE104948 and GSE108109 came from glomerular compartments, samples of GSE104954 and GSE108112 from tubulointerstitial compartments. GSE108113 dataset was composed by GSE108109 and GSE108112. The detail of relevant datasets is shown in Table 1 .
Human kidney tissue was treated as previously illustrated [17 (link)]. In brief, obtained kidney tissue was stored in RNAlater (ThermoFisher) and microdissected into tubulointerstitial and glomerular compartments [18 ]. Transcriptional data were employed to evaluate reliability of microdissection by reaching to 16–64 folds enrichment of glomerular selective or tubulointerstitial selective transcripts in each independent compartment [18 ].
Human kidney tissue was treated as previously illustrated [17 (link)]. In brief, obtained kidney tissue was stored in RNAlater (ThermoFisher) and microdissected into tubulointerstitial and glomerular compartments [18 ]. Transcriptional data were employed to evaluate reliability of microdissection by reaching to 16–64 folds enrichment of glomerular selective or tubulointerstitial selective transcripts in each independent compartment [18 ].
3
Cancer Microarray Gene Expression Analysis
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This study used 14 publicly available cancer microarray gene expression datasets downloaded, in the format of SOFT file, from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (Table 1 ). The datasets originated from the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array platform (GPL570). The samples were classified by sample status (normal vs cancerous). The data in the SOFT file was preprocessed and normalized by the submitting laboratory.
4
Meta-analysis of Alopecia Biomarkers
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The aim of the meta-analysis was to identify potential biomarkers for alopecia to effectively diagnose the causes of hair loss. Alopecia-related expression datasets were identified and retrieved from the Gene Expression Omnibus (GEO) database excluding the non-human studies. Information extracted from each dataset covers GEO accession number, sample type, platform, number of samples, and gene expression data. This study examines the genes commonly covered by hgu133plus2 chips. In these datasets, the Affymetrix Gene Chip Human Genome U133Plus2.0 Array platform and the annotation information (hgu133plus2) of probes were used to check differentially expressed genes. R-platform and BioConductor packages including Affy, AffyQCReport, AffyRNADegradation, AnnotationDbi, Annotate, Biobase, Limma, hgu133a2cdf and hgu133plus2cdf were employed to evaluate the statistical significance of the results (Additional file 1 : Fig. S1).
5
Sex-specific gene expression in HCC
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Gene expression profiles that provided information concerning the sex features of subjects, including GSE19665 (22 (link)), GSE23343 (23 (link)) and GSE9843 (24 (link)) were downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo ), a public functional genomics dataset with high-throughput gene expression data chips and microarrays (21 (link)). The selection was based on a GeneChip Human Genome U133 Plus 2.0 Array platform (Affymetrix; Thermo Fisher Scientific, Inc.). The datasets comprised 108 tissue samples, including normal liver samples from 4 female subjects and 13 male subjects, in addition to 28 and 63 HCC samples from female and male subjects, respectively.
Furthermore, raw tissue mRNA expression data and corresponding clinical information from patients with HCC were downloaded from The Cancer Genome Atlas (TCGA;http://cancergenome.nih.gov ). The selection included 22 and 28 paired samples of normal liver tissues and corresponding HCC samples from 117 male and 245 female subjects with HCC, respectively.
Furthermore, raw tissue mRNA expression data and corresponding clinical information from patients with HCC were downloaded from The Cancer Genome Atlas (TCGA;
6
Exploring HOXA11-AS Co-Expression Networks
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To further analyze the potential pathways associated with HOXA11-AS, we used an open-access resource, Multi Experiment Matrix (MEM, http://biit.cs.ut.ee/mem/index.cgi )21 (link), 22 (link), to interactively explore the co-expressed genes for HOXA11-AS based on an Affymetrix Gene Chip Human Genome U133 Plus 2.0 Array platform. Then, functional enrichment analyses at the GO and KEGG pathway levels were conducted to infer HOXA11-AS co-expressed gene function by respectively using the DAVID Bioinformatics Tool (https://david.ncifcrf.gov/ , version 6.7)23 (link), 24 (link) and KOBAS 2.0 (http://kobas.cbi.pku.edu.cn/ )54 (link). Both the GO enrichment and KEGG pathway analysis55 (link)–57 (link) were performed by Fischer’s exact test. In this process, three independent categories derived from the GO analysis were included: biological process (BP), cellular component (CC) and molecular function (MF).
7
Microarray Analysis of Bladder Cancer
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Human microarray expression data were mined from the GEO database (GSE24152) which was run on the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array platform. [15 (link)] GSE24152 was selected because of similar technology (Affymetrix platform) and inclusion of normal human bladder and treatment naive human iUC samples. This platform contains a complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts. The dataset included microarray expression data from human normal bladder (n = 7) and iUC samples (n = 8). In silico validation of this dataset was conducted against larger datasets GSE31684 and GSE5287 (95.6% overlap) to further confirm the agreement of the selected dataset against larger ones reported. The raw data (GSE24152) were processed and analyzed as described for canine samples using GeneSpring GX 12.6.1 (Agilent Technologies, Santa Clara, CA).
8
Gene Expression and DNA Methylation Analysis of 5-HTT
9
Microarray-based Gene Expression Analysis
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Total RNA was extracted using TRIzol Reagent (Life technologies, Carlsbad, CA, US) according to the manufacturer’s instructions. RNA integrity was checked by an Agilent Bioanalyzer 2100. Gene expression was performed by Affymetrix GeneChip Human Genome U133 Plus 2.0 array platform. The hybridization occurred in a Hybridization Oven 645 (Affymetrix Inc.). The chips were then washed and stained in a Fluidics Station 450 (Affymetrix Inc.) and the arrays were scanned with a Gene Chip Scanner 3000 and Command Console Software 3.1 with default settings. The selection criterion was > 1.3-fold difference in expression (difference in upregulated expression > 1.3-fold; difference in downregulated expression < 0.77-fold). Hierarchical clustering of samples was performed using an average linkage algorithm using TIGR Multiexperiment Viewer (The Institute for Genomic Research, Rockville, MD, USA).
10
Chloride Channel Regulation in Rectal Cancer
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To determine the significant chloride channel associated with the response of CCRT, the transcriptome dataset which was derived from tissues of rectal cancers (n=46) and deposited in Gene Expression Omnibus (GSE35452) was assessed. According to the response to neoadjuvant CCRT, the tumors were categorized into “responder” and “non-responder”. Nexus Expression 3 software (BioDiscovery) was utilized to analyze all probe sets from raw files of GeneChip® Human Genome U133 Plus 2.0 array platform (Affymetrix) without filtering or pre-selection. By comparing responder and non-responder, with special attention to chloride channel activity (GO:0005254), statistically significant genes were examined. Those transcripts with P-value <0.01 and fold change of log2-transformed expression >0.1 were designated for further analyses.
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