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2.0 microarray

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The 2.0 microarray is a high-density array designed for gene expression analysis. It enables the simultaneous measurement of thousands of gene transcripts in a single experiment.

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HGU133 Plus 2.0 microarrays (21 citations) HG-U133 plus 2.0 Genechip microarrays (10 citations) Mouse Genome 430A 2.0 microarrays (3 citations) U133 Plus 2.0 GeneChip microarrays (3 citations) Mouse Expression 430 2.0 microarrays (2 citations) Human Genome U133 plus 2.0 GeneChip oligonucleotide microarrays (2 citations) U133A 2.0 microarrays (2 citations) GeneChip™ Human Transcriptome Array 2.0 microarrays (2 citations) GeneChip Mouse Genome 430A 2.0 microarrays (2 citations) Human Genome U133 Plus 2.0 GeneChips® microarrays (2 citations)

3 protocols using 2.0 microarray

1

Profiling Metastatic Breast Cancer Transcriptomes

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To acquire the mRNA and lncRNA expression profiles of bone metastasis, lung metastasis and liver metastasis of breast cancer tissues, datasets in GEO database with the following criteria were retrieved: datasets should be whole-genome mRNA/lncRNA expression profile by array; these data were derived from bone metastasis, lung metastasis and liver metastasis of breast cancer tissues; datasets were normalized or original. After screening, four mRNA datasets and two lncRNA datasets were enrolled in this study and shown in Table 1.

List of mRNA/lncRNA study samples from GEO database

GEO accessionPlatformsLiver metastasisLung metastasisBone metastasisYearcountry
mRNA
 GSE14020GPL96 [HG-U133A] Affymetrix human genome U133A array51682009USA
GPL570[HG-U133_Plus_2] Affymetrix human genome U133 plus 2.0 array0410
 GSE54323GPL570[HG-U133_Plus_2] Affymetrix human genome U133 plus 2.0 array70142015Sweden
 GSE46141GPL10379 Rosetta/Merck human RSTA custom Affymetrix 2.0 microarray [HuRSTA-2a520709]16252013Sweden
lncRNA
 GSE14020GPL570[HG-U133_Plus_2] Affymetrix human genome U133 plus 2.0 array04102009USA
 GSE54323GPL570[HG-U133_Plus_2] Affymetrix human genome U133 plus 2.0 array70142015Sweden
Zhang Y., Huang X., Liu J., Chen G., Liu C., Zhang S, & Li J. (2021). New insight into long non-coding RNAs associated with bone metastasis of breast cancer based on an integrated analysis. Cancer Cell International, 21, 372.
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2

TCGA and TCC data analysis of MAFG in NSCLC

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The Cancer Genome Atlas (TCGA) data: We obtained RNA sequencing data for the MAFG of 984 NSCLC tumors from the TCGA. The raw reads were quantified by RSEM21 (link) in order to determine the read counts for each gene and miRNA (calculated separately). Then, we filtered out genes and miRNAs having less than one count-per-million reads in all samples. The normalization process was performed with trimmed mean of M values22 to obtain the MAFG sequence count data in all patients.
Total Cancer Care (TCC): We obtained MAFG gene expression data for 1035 lung cancer samples from the Moffitt Cancer Center Total Cancer Care Bioreposi-tory23 that were assayed on a custom Affymetrix 2.0 microarray. Normalized intensity values for MAFG probe sets were obtained and the probe with highest average intensity was retained for gene expression analysis.
VERA-PUENTE O., RODRIGUEZ-ANTOLIN C., SALGADO-FIGUEROA A., MICHALSKA P., PERNIA O., REID B.M., ROSAS R., GARCIA-GUEDE A., SACRISTÁN S., JIMENEZ J., ESTEBAN-RODRIGUEZ I., MARTIN M.E., SELLERS T.A., LEÓN R., GONZALEZ V.M., DE CASTRO J, & DE CACERES I.I. (2018). MAFG is a potential therapeutic target to restore chemosensitivity in cisplatin-resistant cancer cells by increasing reactive oxygen species. Translational research : the journal of laboratory and clinical medicine, 200, 1-17.
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3

TCGA and TCC data analysis of MAFG in NSCLC

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The Cancer Genome Atlas (TCGA) data: We obtained RNA sequencing data for the MAFG of 984 NSCLC tumors from the TCGA. The raw reads were quantified by RSEM21 (link) in order to determine the read counts for each gene and miRNA (calculated separately). Then, we filtered out genes and miRNAs having less than one count-per-million reads in all samples. The normalization process was performed with trimmed mean of M values22 to obtain the MAFG sequence count data in all patients.
Total Cancer Care (TCC): We obtained MAFG gene expression data for 1035 lung cancer samples from the Moffitt Cancer Center Total Cancer Care Bioreposi-tory23 that were assayed on a custom Affymetrix 2.0 microarray. Normalized intensity values for MAFG probe sets were obtained and the probe with highest average intensity was retained for gene expression analysis.
VERA-PUENTE O., RODRIGUEZ-ANTOLIN C., SALGADO-FIGUEROA A., MICHALSKA P., PERNIA O., REID B.M., ROSAS R., GARCIA-GUEDE A., SACRISTÁN S., JIMENEZ J., ESTEBAN-RODRIGUEZ I., MARTIN M.E., SELLERS T.A., LEÓN R., GONZALEZ V.M., DE CASTRO J, & DE CACERES I.I. (2018). MAFG is a potential therapeutic target to restore chemosensitivity in cisplatin-resistant cancer cells by increasing reactive oxygen species. Translational research : the journal of laboratory and clinical medicine, 200, 1-17.
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