Gpl96 platform

Manufactured by Thermo Fisher Scientific

The GPL96 platform is a high-throughput, automated nucleic acid extraction system designed for use in clinical and research laboratories. It utilizes magnetic bead-based technology to efficiently extract and purify DNA, RNA, or viral nucleic acids from a variety of sample types. The GPL96 platform is capable of processing up to 96 samples simultaneously, providing a streamlined and consistent workflow to support various applications, such as diagnostic testing, genomic research, and molecular biology studies.

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Lab products found in correlation

Human genome u133a array, by Thermo Fisher Scientific (6 mentions) Hg u133a, by Thermo Fisher Scientific (3 mentions)

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GPL96 (4 citations)

7 protocols using gpl96 platform

Integrative Analysis of Breast Cancer Transcriptomes

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Two gene expression datasets, GSE2034 (14 (link)) and GSE25066 (15 (link)), were downloaded from ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). Dataset GSE2034 included 286 breast cancer samples and dataset GSE25066 included 508 breast cancer samples. The two gene expression datasets were obtained using Affymetrix GPL96 platform.
Normalization was performed with rma from the affy package (16 (link)) in R (R 3.2.0; https://www.r-project.org/) and then log₂ conversion was applied. Probes were mapped onto genes according to annotation files. Probes mapping to the same gene were averaged as the expression level for the gene.

Shi H., Zhang L., Qu Y., Hou L., Wang L, & Zheng M. (2017). Prognostic genes of breast cancer revealed by gene co-expression network analysis. Oncology Letters, 14(4), 4535-4542.

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Downloading and Preprocessing GEO Dataset GSE2240

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The Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo, RRID:CVCL_VR24) is a public repository that provides access to high-throughput genomic datasets (Wang et al., 2019 (link)). We downloaded the GSE2240 datasets (Affymetrix GPL 96 platform. Affymetrix Human Genome U133A Array) from the GEO database to use in our analysis. Furthermore, the probes were converted into corresponding gene symbols based on the platform annotation information from the published data. The GSE2240 datasets contained 10 AF tissue samples and 20 SR tissue samples.

Li Q., Lai Y., Gao X., Li X., Deng C.Y., Guo H., Zhao J., Yang H., Xu Y., Wu S., Xue Y, & Rao F. (2021). Involvement of plasminogen activator inhibitor-1 and its related molecules in atrial fibrosis in patients with atrial fibrillation. PeerJ, 9, e11488.

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Comparative Transcriptomics of Melanoma Progression

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GEO (http://www.ncbi.nlm.nih.gov/geo) [7 (link)] is a gene expression database created by NCBI, which contains high-throughput gene expression data submitted by research institutes worldwide. Three microarray datasets (GSE8401, GSE46517, and GSE7956) were downloaded from it (Affymetrix GPL96 platform, Affymetrix [HG-U133A] Affymetrix Human Genome U133A Array). The GSE8401 dataset includes 31 primary melanoma samples and 52 metastatic melanoma samples. GSE46517 consists of 31 primary melanoma samples and 73 metastatic melanoma samples. GSE7956 contains 10 poorly metastatic melanoma samples and 29 highly metastatic melanoma samples.

Su W., Guan Y., Huang B., Wang J., Wei Y., Zhao Y., Jiao Q., Ji J., Yu D, & Xu L. (2020). Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis. BMC Cancer, 20, 863.

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Cervical Cancer Transcriptome Analysis

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Cervical cancer gene expression data that were publicly available and reported in full clinical annotation were systematically searched. The microarray datasets, GSE9750 and GSE7803 (Affymetrix GPL96 platform, Affymetrix Human Genome U133A Array), and TCGA-cervical squamous cell carcinoma (CESC) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo) and UCSC Xena browser (https://xenabrowser.net/datapages/). The GSE9750 dataset contains 24 normal cervical tissue samples and 28 cervical cancer tissue samples. The GSE7803 dataset contains 10 normal cervix tissue samples, 7 HSIL tissue samples and 21 cervical cancer tissue samples. The DEGs, with log fold change (FC) >3 and adj. P-value <0.01, in the mRNA expression profiling sets, GSE9750 and GSE7803, were selected with GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).

Liu L., Shi W., Xiao X., Wu X., Hu H., Yuan S., Liu K, & Liu Z. (2021). BCG immunotherapy inhibits cancer progression by promoting the M1 macrophage differentiation of THP-1 cells via the Rb/E2F1 pathway in cervical carcinoma. Oncology Reports, 46(5), 245.

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Melanoma Transcriptome Profiling from GEO

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2.1 Data collection GEO (http://www.ncbi.nlm.nih.gov/geo) [7] is a gene expression database created by NCBI, which contains high-throughput gene expression data submitted by research institutes worldwide. Three microarray datasets (GSE8401, GSE46517, and GSE7956) were downloaded from it (Affymetrix GPL96 platform, Affymetrix [HG-U133A] Affymetrix Human Genome U133A Array). The GSE8401 dataset includes 31 primary melanoma samples and 52 metastatic melanoma samples. GSE46517 consists of 31 primary melanoma samples and 73 metastatic melanoma samples. GSE7956 contains 10 poorly metastatic melanoma samples and 29 highly metastatic melanoma samples.

Su W., Guan Y., Huang B., Wang J., Wei Y., Zhao Y., Jiao Q., Ji J., Yu D., & Xu L. (2020). Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis.

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Melanoma Transcriptome Profiling from GEO

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Su W., guan y., Huang B., wang j., Wei Y., Zhao Y., Jiao Q., Ji J., Yu D., & Xu L. (2020). Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis.

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Melanoma Metastasis Gene Expression Profiling

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GEO (http://www.ncbi.nlm.nih.gov/geo)[8] is a gene expression database created by NCBI, which contains high-throughput gene expression data submitted by research institutes worldwide. Three microarray datasets (GSE8401, GSE46517, and GSE7956) were downloaded from it (Affymetrix GPL96 platform, Affymetrix [HG-U133A] Affymetrix Human Genome U133A Array). The GSE8401 dataset includes 31 primary melanoma samples and 52 metastatic melanoma samples. GSE46517 consists of 31 primary melanoma samples and 73 metastatic melanoma samples. GSE7956 contains 10 poorly metastatic melanoma samples and 29 highly metastatic melanoma samples.

Su W., guan y., Huang B., wang j., Wei Y., Zhao Y., Jiao Q., Ji J., Yu D., Su W., Guan Y., Huang B., Su W., Guan Y., & Huang B. (2020). Bioinformatics analysis reveals key genes and pathways that promote melanoma metastasis.

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