The GSE85195 dataset (17 (link)) was downloaded from the NCBI Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/ ). The dataset included 15 OL, 24 early (stage 1–2) OSCC and 10 late (stage 3–4) OSCC samples; these samples were later divided into OL, early and late groups, respectively. The dataset was generated using the Agilent-014850 Whole Human Genome Microarray 4×44K G4112F platform (Agilent Technologies, Inc.).
Agilent 014850 whole human genome microarray 4 44k g4112f
Manufactured by Agilent Technologies
Sourced in United States
The Agilent-014850 Whole Human Genome Microarray 4 × 44K G4112F is a DNA microarray designed for whole human genome analysis. It contains approximately 44,000 probes that cover the majority of known and predicted genes in the human genome. The microarray is designed for high-throughput gene expression profiling and can be used to analyze the expression levels of thousands of genes simultaneously.
Automatically generated - may contain errors
Lab products found in correlation
Affymetrix human genome u133 plus 2.0 array, by Thermo Fisher Scientific (4 mentions)
Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (3 mentions)
Human genome 1.0 st array, by Agilent Technologies (2 mentions)
Agilent 012097 human 1a microarray v2 g4110b, by Agilent Technologies (2 mentions)
Human genome u133 plus 2.0 array, by Agilent Technologies (2 mentions)
Humanht 12 v4.0 expression beadchip, by Illumina (2 mentions)
Affymetrix human gene 1.1 st array, by Thermo Fisher Scientific (1 mentions)
Hg u133 plus 2 affymetrix human genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
Human v2 microrna expression beadchip, by Illumina (1 mentions)
Human genome u133a array, by Agilent Technologies (1 mentions)
Affymetrix human genome u133 plus 2.0 array, by Agilent Technologies (1 mentions)
Hiseq rna seq platform, by Illumina (1 mentions)
Agilent 028004 sureprint g3 human ge 8 60k microarray, by Agilent Technologies (1 mentions)
Humanht 12 wg dasl v4.0 r2 expression beadchip, by Illumina (1 mentions)
Affymetrix human genome u133a 2.0 array, by Thermo Fisher Scientific (1 mentions)
Affymetrix human gene 1.0 st array, by Thermo Fisher Scientific (1 mentions)
Affymetrix human genome u133a array, by Thermo Fisher Scientific (1 mentions)
Gpl4133 platform, by Agilent Technologies (1 mentions)
Agilent 039494 sureprint g3 human ge v2 8 60k microarray 039381, by Agilent Technologies (1 mentions)
Human genome u133 plus 2.0 array platform, by Thermo Fisher Scientific (1 mentions)
47 protocols using agilent 014850 whole human genome microarray 4 44k g4112f
1
Oral Squamous Cell Carcinoma Transcriptome Analysis
2
Identifying IPF Biomarkers in Blood
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
First, we searched the GEO database (https://www.ncbi.nlm.nih.gov/geo/ ) for keywords such as “idiopathic pulmonary fibrosis”, “survival”, “blood”, etc. Then, by combining samples for survival information, we eventually included the GSE28042 and GSE93606 datasets into the study. GSE28042 was used as the experimental dataset and GSE93606 was used as the validation dataset. The GSE28042 dataset contains the gene expression profiles of peripheral blood mononuclear cell (PBMC) and their corresponding clinical data of 75 IPF patients and 19 healthy people. The probes were converted to corresponding gene symbols by referring to the annotation information of the GPL6480 [Agilent-014850 Whole Human Genome Microarray 4 × 44K G4112F (Probe Name version)] platform. The GSE93606 dataset contains peripheral whole blood gene expression profiles and corresponding clinical data of 60 IPF patients and 20 healthy subjects. The probes were converted to the corresponding gene symbols by referring to the annotation information of GPL11532 [Hugene-11-ST] Affymetrix Human Gene 1.1 ST Array [transcript (Gene) version] platform.
3
Comparative Analysis of ccRCC Transcriptomes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
From GEO online database [16 ], we picked four ccRCC cDNA expression profiles GSE53757 [17 ], GSE53000 [18 ], GSE71963 [19 ] and GSE68417 [20 ] based on the sample number (only the profiles that contain at least 40 samples covering both cancer and normal tissues were considered). And of the four profiles, GSE53757 was based on agilent GPL570 platform [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, containing 72 ccRCC and 72 kidney normal samples. And GSE53000 profile was based on agilent GPL6244 platform [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array, containing 56 ccRCC samples and 6 kidney normal tissues. Meanwhile, GSE71963 was based on agilent GPL6480 platform Agilent-014850 Whole Human Genome Micro array 4×44K G4112F and contains 32 ccRCC and 16 normal kidney samples, as well as GSE68417 which was based on agilent GPL6244 platform [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array, contains 29 ccRCC and 14 normal samples(Detailed information and accessing weblink in Additional file 1 : Table S1).
4
Comparative Analysis of Intracranial Aneurysm Transcriptomes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The gene expression datasets are obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/ ). Three gene expression datasets (GSE13353, GSE15629 and GSE54083) of IAs are selected. Among them, GSE13353 is based on platform GPL570([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE15629 is based on platform GPL6244([HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]), and GSE54083 is based on platform GPL4133(Agilent-014850 Whole Human Genome Microarray 4 × 44 K G4112F (Feature Number version)). The data of GSE13353 dataset is submitted by Kurki MI et al., including 11 ruptured intracranial aneurysm samples (RIAs) and 8 unruptured intracranial aneurysm samples (UIAs) (Kurki et al., 2011 (link)). The data of GSE15629 dataset is submitted by Pera J et al., including 8 RIAs and 6 UIAs(Pera et al., 2010 (link)). The data of GSE54083 dataset is submitted by Nakaoka H et al., which consisted of 8 RIAs and 5 UIAs (Nakaoka et al., 2014 (link))..(Table 1 )
5
Transcriptomic Analysis of Crohn's Disease
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
GEO (http://www.ncbi.nlm.nih.gov/geo ) (Edgar et al., 2002 (link)) is a public functional genomics data repository of high throughput gene expression data, chips and microarrays. The GSE75214 (Vancamelbeke et al., 2017 (link)) and GSE102133 (Verstockt et al., 2019 (link)) datasets generated using the Affymetrix GPL6244 platform, (Affymetrix Human Genome 1.0 ST Array), and GSE179285 (Keir et al., 2021 (link)) generated on the GPL6480 platform (Agilent-014850 Whole Human Genome Microarray 4 × 44K G4112F) were downloaded from GEO. Annotated information from the platform was used to convert the probes to the corresponding gene symbols. The GSE179285 dataset contained 47 CD intestinal mucosa tissue samples and 31 controls; the GSE75214 dataset contained 59 CD samples and 22 healthy controls; and the GSE102133 dataset contained 65 intestinal mucosal biopsies from CD patients and 12 intestinal mucosal tissues from controls.
6
Comparative Analysis of Gene and miRNA Expression in CAD
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The gene expression profiles of GSE20680 (18 (link)) and GSE12288 (19 (link)) were downloaded from the gene expression omnibus (GEO) database in NCBI (National Center for Biotechnology Information; http://www.ncbi.nlm.nih.gov/geo/ ) based on the platforms of GPL4133 Agilent-014850 Whole Human Genome Microarray 4×44K G4112F (Feature Number version) and GPL96 [HG-U133A] Affymetrix Human Genome U133A Array, respectively. The dataset of GSE20680 contained 143 CAD and 52 control samples, and that of GSE12288 included 110 CAD and 112 control samples. In addition, the miRNA expression profile data of GSE28858 (20 (link)) was comprised of 12 samples from patients with premature CAD and 12 age- and gender-matched healthy control samples. It was downloaded from the GEO database in NCBI based on the platform of GPL8179 Illumina Human v2 MicroRNA expression beadchip.
The gene profile data of GSE20680 was preprocessed using Agilent Feature Extraction software (version 9.5.3.1; Aglient Technologies, Inc. Santa Clara, CA, USA) (21 (link)). The CEL file data of GSE12288 was preprocessed using the robust multi-array analysis method from the affy package in R (22 (link)). If a gene had several probes the mean expression value was selected. Additionally, miRNA IDs from the preprocessed expression matrix of GSE28858 were transformed into the miRNA symbols.
The gene profile data of GSE20680 was preprocessed using Agilent Feature Extraction software (version 9.5.3.1; Aglient Technologies, Inc. Santa Clara, CA, USA) (21 (link)). The CEL file data of GSE12288 was preprocessed using the robust multi-array analysis method from the affy package in R (22 (link)). If a gene had several probes the mean expression value was selected. Additionally, miRNA IDs from the preprocessed expression matrix of GSE28858 were transformed into the miRNA symbols.
7
Gene Expression Analysis Using Public Datasets
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Data sets of our study were all from the Gene Expression Omnibus (GEO) public database (https://www.ncbi.nlm.nih.gov/geo/ ) and 4 sets of gene expression profiling chips (GEPC) are selected, including GSE38959 (GPL4133; Agilent-014850 Whole Human Genome Microarray 4 × 44 K G4112F), GSE53752 (GPL7264; Agilent-012097 Human 1A Microarray (V2) G4110B), GSE45827 and GSE65194 (GPL570; [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array).
8
Differential Expression Analysis of COPD Transcriptome
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The normalized expression matrix of the microarray dataset GSE38974 contained 23 COPD and 9 normal lung tissue samples and was obtained with the GPL4133 platform (Agilent-014850 Whole Human Genome Microarray 4 × 44K G4112F). This dataset was used to screen differentially expressed NRGs. The gene expression levels in the high-throughput sequencing dataset GSE57148, which included 98 COPD and 91 normal lung tissue samples and was based on the GPL11154 platform (Illumina HiSeq 20009, Homo sapiens), were normalized using transcripts per million (TPM). The PCA plot was generated using the “ggplot2” package of R software (version 4.2.1) [19 (link)]. All data used in the study are publicly accessible in the GEO database (http://www.ncbi.nlm.nih.gov/geo/ , accessed on 9 June 2022) [20 (link)]. Detailed information on the datasets is shown in Table 1 .
9
Integrative Analysis of GBM Transcriptome
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Original data were collected from GSE22866 and TCGA. The expression profiles of related genes were downloaded from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/ ). GSE22866 data [7 (link)] including the information of 40 tumor tissue samples and 6 normal tissue samples, were processed by Agilent-014850 Whole Human Genome Microarray 4×44K G4112F. Robust multi-array average (RMA) approach was adopted for background correction and normalization [8 (link)]. The original GEO data were then transformed into expression values using affy R package [9 (link)]. The genomic and clinical data of GBM were downloaded from TCGA (https://cancergenome.nih.gov/ ) and the RNA sequencing data from Illumina Hi-SeqRNA-Seq platform. The flow chart of the whole research is shown in Figure 1 .
10
Differential Gene Expression in Medulloblastoma
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA-seq and microarray data were retrieved from the GEO database (http://www.ncbi.nlm.nih.gov/geo/ ). Microarray data comprised GSE35493 (based on Affymetrix Human Genome U133 Plus 2.0 Array, GPL570) (11 (link)) and GSE39182 (based on Agilent-014850 Whole Human Genome Microarray 4×44K G4112F, GPL6480) (12 (link)). GSE35493 included 21 MB and 9 normal brain samples. GSE39182 included 20 MB and 5 normal samples. In addition, RNA-seq data GSE148389 (based on NextSeq 550, GPL21697) contained 14 normal and 26 tumor tissues (13 (link)). All probes were annotated by annotation files. Data processing was performed using R 3.6.0 software (https://www.r-project.org/ ). DEGs between MB and normal samples in the GSE35493 and GSE39182 microarray datasets were screened using the Limma package (14 (link)), and GSE148389 RNA-seq data were analyzed using the edgeR package (15 (link)). An adjusted P<0.05 and |log2 fold change (FC)|≥1 were set as thresholds to identify the DEGs. Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn/ ) were utilized to detect and present the common DEGs among the three datasets.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!