Stroke-related human blood mRNA expression data (GSE16561 and GSE58294) were collected from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo ) datasets. The GSE16561 dataset included 39 patients and 24 controls. Each sample was tested using the Illumina HumanRef-8 v3.0 Expression BeadChip (Illumina, San Diego, CA, USA). The GSE58294 dataset contained 69 ischemic stroke samples and 23 controls. The ischemic stroke samples collected at 3 different time point within 3 h (prior to treatment), 5 h and 24 h (after treatment) after stroke onset (n = 23). All 92 samples were tested using the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA).
Humanref 8 v3.0 expression beadchip
Manufactured by Illumina
Sourced in United States
The HumanRef-8 v3.0 expression beadchip is a high-density microarray platform designed for gene expression analysis. It provides comprehensive coverage of the human transcriptome, enabling researchers to measure the expression levels of over 25,000 well-annotated genes simultaneously.
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Lab products found in correlation
Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (3 mentions)
Humanht 12 v4.0 expression beadchip, by Illumina (3 mentions)
Human genome u133 plus 2, by Thermo Fisher Scientific (2 mentions)
Human genome u133 plus 2.0 array, by Illumina (2 mentions)
Affymetrix human genome u133 plus 2.0 array, by Thermo Fisher Scientific (2 mentions)
Hiscansq, by Illumina (1 mentions)
Hiseq 2500, by Illumina (1 mentions)
Affymetrix human exon 1.0 st array, by Thermo Fisher Scientific (1 mentions)
Human genome 1.0 st array, by Thermo Fisher Scientific (1 mentions)
Ht hg u133 pm array, by Thermo Fisher Scientific (1 mentions)
Nextseq 500, by Illumina (1 mentions)
Humanmethylation450 beadchip, by Illumina (1 mentions)
Humanref 8 v2.0 expression beadchip, by Illumina (1 mentions)
Human genome u133a array, by Thermo Fisher Scientific (1 mentions)
Hiseq 2000, by Illumina (1 mentions)
Blood rna tubes, by Illumina (1 mentions)
28 protocols using humanref 8 v3.0 expression beadchip
1
Stroke-Related Blood mRNA Expression Profiles
2
Preprocessing Microarray Data for CRC Analysis
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Data preprocessing is a data mining technique that involves transforming raw data into an understandable format. The GSE110224 and GSE25070 microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/ (accessed on 1 May 2021)). The GSE110224 dataset was based on GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array with 34 samples (17 patients with CRC and 17 adjacent samples). The GSE25070 dataset, based on the Illumina HumanRef-8 v3.0 expression bead chip, included 26 CRC samples and 26 adjacent non-tumor colorectal tissue samples. The raw data were corrected and quantile-normalized with the affy package of R 3.4.1 in Bioconductor [8 (link),9 (link)]. The annotation file published by Affymetrix was applied to assign probes to gene IDs and symbols. Data of probe IDs that could not be converted were excluded. Then, the average expression data of identifiers were obtained for each sample. The heatmap was plotted using the pheatmap R package for the CTLA-4 gene in two different CRC datasets.
3
Integrative Analysis of HNSCC Transcriptomes
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The original datasets comparing the mRNA expression profiles between tumors and adjacent normal tissues were obtained from the three GEO databases [GSE30784 (containing 167 oral squamous cell carcinoma, 17 dysplasia, and 45 normal oral tissues), GSE37991 (containing 40 male oral squamous cell carcinoma biopsies), and GSE65858 (containing 290 HNSCC biopsies)] and a TCGA dataset (containing 498 HNSCC biopsies). The clinical samples from the TCGA database with complete clinical information of patients were selected. The microarray data of GSE30784, GSE37991, and GSE65858 were based on GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array), GPL6883 (Illumina HumanRef-8 v3.0 expression beadchip), and GPL10558 (Illumina HumanHT-12 V4.0 expression beadchip), respectively. The corresponding clinical information of patients with HNSCC was also acquired from the TCGA database (up to July 19, 2019). A total of 498 HNSCC patients with detailed follow-up time were included for the following analyses.
4
Differential Gene Expression in T2DM
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The dataset GSE26168 based on the GPL6883 platform (Illumina HumanRef-8 v3.0 expression bead chip) was downloaded from GEO. A total of 9 T2DM samples and 8 normal samples were analyzed.
5
Acute cerebral infarction gene expression analysis
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Acute cerebral infarction expression profile datasets GSE16561 (Barr et al., 2010 (link)) and GSE110993 (Tiedt et al., 2017 (link)) with reliable sample sources were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/ ) database by using the GEO query package (Davis and Meltzer, 2007 (link))of R software (version 3.6.6). The samples in the datasets are all from Homo sapiens. The data in the two datasets were generated using different platforms: GPL6883 Illumina HumanRef-8 v3.0 expression beadchip and GPL15456 Illumina HiScanSQ respectively. GSE16561 dataset includes whole blood samples from 39 patients with acute cerebral infarction and 24 healthy controls. The GSE110993 dataset includes whole blood samples from 20 patients with acute cerebral infarction and 20 healthy patients for inclusion. The raw data were converted into an expression matrix and corrected for background and normalized by the limma package (Ritchie et al., 2015 (link)). Afterwards, the batch effect was removed in sva package (Leek et al., 2012 (link)). A flow diagram for the present analysis is shown in Figure 1 .
6
Transcriptional Profiles of Allergic Rhinitis
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GSE43523 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43523 ), a dataset derived from nasal epithelial cells, and GSE75011 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75011 ), a dataset derived from Th2-enriched CD4+ T cells from peripheral blood, were obtained from the GEO database. GSE43523, which includes seven samples from patients with seasonal AR (SAR) and five samples from non‑allergic healthy controls, was derived from the GPL6883 platform (Illumina HumanRef-8 v3.0 expression bead chip), and GSE75011, which includes 25 samples from patients with AR and 15 samples from healthy controls, was derived from the GPL16791 platform (Illumina HiSeq 2500) [11 (link)]. The flow chart of our study is shown in Additional file 1 : Figure S1.
7
FRZB Expression in Comprehensive HNSCC Analysis
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The sequence data and the relative clinical information was collected from The
Cancer Genome Atlas (TCGA). As the largest cancer genetic information database
for large-scale genome sequencing and other data like proteomic, epigenetic,
transcriptomic, and genomic, TCGA database includes 33 types of cancer. As
Supplementary Table
S1 shows, we found the expression of FRZB
and complete clinical data for 499 HNSCC patients. TIMER2 webserver was employed
for analyzing FRZB expression of pan-cancer (11 (link)). In order to determine the expression of FRZB in HNSCC patients,
the datasets GSE30784, GSE25099, and GSE37991 were collected from the Gene
Expression Omnibus (GEO). GSE30784 includes 167 oral squamous cell carcinoma
(OSCC) samples and 45 adjacent normal samples from the GPL570 platform
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. The GPL5175
platform [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array was used to obtain
GSE25099, which includes 22 adjacent normal samples and 57 OSCC samples.
GSE37991 was from GPL6883 Illumina HumanRef-8 v3.0 expression bead chip, and
includes 40 OSCC and 40 adjacent normal samples. FRZB expression was analyzed in
different clinical subgroups comprehensively by using UALCAN webserver (12 (link)).
Cancer Genome Atlas (TCGA). As the largest cancer genetic information database
for large-scale genome sequencing and other data like proteomic, epigenetic,
transcriptomic, and genomic, TCGA database includes 33 types of cancer. As
S1
and complete clinical data for 499 HNSCC patients. TIMER2 webserver was employed
for analyzing FRZB expression of pan-cancer (11 (link)). In order to determine the expression of FRZB in HNSCC patients,
the datasets GSE30784, GSE25099, and GSE37991 were collected from the Gene
Expression Omnibus (GEO). GSE30784 includes 167 oral squamous cell carcinoma
(OSCC) samples and 45 adjacent normal samples from the GPL570 platform
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. The GPL5175
platform [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array was used to obtain
GSE25099, which includes 22 adjacent normal samples and 57 OSCC samples.
GSE37991 was from GPL6883 Illumina HumanRef-8 v3.0 expression bead chip, and
includes 40 OSCC and 40 adjacent normal samples. FRZB expression was analyzed in
different clinical subgroups comprehensively by using UALCAN webserver (12 (link)).
8
Differentially Expressed Genes in Ischemic Stroke
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The transcription profile E-GEOD-16561 (4 (link)) was obtained through EMBI-EBI ArrayExpress database (11 (link)). The data included gene expression profiling of 39 ischemic stroke patients and 24 healthy controls. The platform was: A-MEXP-1172 - Illumina HumanRef-8 v3.0 Expression BeadChip.
Data of the gene chip was read as previously described (12 (link)). The gene expression data was preprocessed by Linear Models for Microarray Data (LIMMA). Robust multi-array average (RMA) was applied to adjust the background and normalize the quantile data (13 (link)). We used a median polish and robust procedure for protecting against outlier probes (14 (link)) and estimating model parameters. The DEG were selected according to the threshold levels: P≤0.01, |log fold-change (FC)| ≥2.
Data of the gene chip was read as previously described (12 (link)). The gene expression data was preprocessed by Linear Models for Microarray Data (LIMMA). Robust multi-array average (RMA) was applied to adjust the background and normalize the quantile data (13 (link)). We used a median polish and robust procedure for protecting against outlier probes (14 (link)) and estimating model parameters. The DEG were selected according to the threshold levels: P≤0.01, |log fold-change (FC)| ≥2.
9
Differential Gene Expression in Aging
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The gene expression profile of GSE37587 was downloaded from the database (gene expression omnibus; http://www.ncbi.nlm.nih.gov/geo/ ). This dataset was based on the GPL6883 platform (Illumina HumanRef-8 v3.0 expression beadchip). The GSE37587 dataset contained 68 samples, including 46 patients who were ≥ 65 years old, and were defined as the old group, and 22 of them were younger than 65 years old and were defined as the young group.
The study was approved by the Ethics Committee of the Nanjing First Hospital.
The study was approved by the Ethics Committee of the Nanjing First Hospital.
10
Transcriptional Profiles of Allergic Rhinitis
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Gene expression profiles were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo ). GSE19187 includes 14 cases of isolated AR without asthma and 11 healthy control samples. The expression profiling of nasal epithelial cells collected by brushing had been performed on the GPL6244 platform (Affymetrix Human Genome 1.0 ST Array);18 (link)
GSE44037 includes five cases of AR and six healthy control samples, based on the GPL13158 platform (Affymetrix HT HG-U133+ PM Array);19 (link)
and GSE43523 includes seven cases of SAR and five healthy control samples, based on the GPL6883 platform (Illumina HumanRef-8 v3.0 expression beadchip). Datasets GSE44037 and GSE43523 were merged as validation data to validate the critical genes. The expression levels of CD44, HLA-DPA1, HLA-DRB1, HLA-DRB5, MUC5B, and CD274 were compared between AR and healthy control samples using the Wilcoxon test. The subject characteristics of the dataset are listed in Supplementary Table 1 and the genes detected by microarray data are listed in Supplementary Table 2. All data are freely available online, and this study did not involve any experiments on humans or animals performed by any of the authors. Ethical approval was not required because this study used publicly available datasets.
GSE44037 includes five cases of AR and six healthy control samples, based on the GPL13158 platform (Affymetrix HT HG-U133+ PM Array);19 (link)
and GSE43523 includes seven cases of SAR and five healthy control samples, based on the GPL6883 platform (Illumina HumanRef-8 v3.0 expression beadchip). Datasets GSE44037 and GSE43523 were merged as validation data to validate the critical genes. The expression levels of CD44, HLA-DPA1, HLA-DRB1, HLA-DRB5, MUC5B, and CD274 were compared between AR and healthy control samples using the Wilcoxon test. The subject characteristics of the dataset are listed in Supplementary Table 1 and the genes detected by microarray data are listed in Supplementary Table 2. All data are freely available online, and this study did not involve any experiments on humans or animals performed by any of the authors. Ethical approval was not required because this study used publicly available datasets.
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