Gene expression and methylation data have been previously published (accession number GSE1159 [27 (link)], GSE9476 [28 (link)], GSE6891 [53 (link)] and GSE12417 [54 (link)] for expression, The Cancer Genome Atlas (TCGA) [50 (link)] for methylation). Briefly, gene expression data were obtained using Affymetrix Human Genome 133 plus 2.0 and U133A Gene Chips. All the designs and quality control for microarray experiment were according to the standard Affymetrix protocols. Expression data for microRNA were from TCGA obtained using whole-genome high-throughput sequencing, which provided 79 CN-AML patients [50 (link)]. In addition, genome-wide methylation levels in these patients were determined using Illumina 450K chips [50 (link)]. Patients with RUNX1 expression values above the median of all patients were classified as having RUNX1high, and the others were considered to have RUNX1low. Levels of ERG, BAALC, LEF1, MN1, WT1, DNMT3B, TCF4, MIR155HG, ITPR2 and MAPKBP1 expression were also determined from the microarray data.
Human genome 133 plus 2
Manufactured by Thermo Fisher Scientific
The Human Genome 133 plus 2.0 is a high-density oligonucleotide array designed for the comprehensive analysis of the human genome. It features over 54,000 probe sets to interrogate the expression of more than 47,000 transcripts and variants, which represents the majority of the human genome.
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4 protocols using human genome 133 plus 2
1
Comprehensive Profiling of CN-AML Patients
2
Integrated Genomic Profiling of CN-AML
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Gene/microRNA expression and methylation data were previously published (accession number GSE1159,GSE9476, GSE30029, GSE6891 and GSE12417 for gene expression). The Cancer Genome Atlas (TCGA) database was used for mRNA/microRNA expression and genome-wide promoter methylation. Briefly, gene expression data were obtained by Affymetrix Human Genome 133 plus 2.0 and U133A Gene Chips. All designs and quality control of the microarray experiment and data normalization were in line with the standard Affymetrix protocols. RNA-Seq data of mRNA/microRNA and genome-wide promoter methylation levels were derived from TCGA obtained by whole-genome high-throughput sequencing and Illumina 450 K chips, respectively, which provided 73 CN-AML patients with all data for mRNA, microRNA and methylation. Patients with MAP7 expression values (whether microarray in GEO or RNA-Seq in TCGA) above the median for all patients were classified as having MAP7high, and the others were considered to have MAP7low. ERG, BAALC, LEF1, WT1, DNMT3A, DNMT3B, MAPKBP1, ITPR2, and ATP1B1 expression levels were also determined from the microarray data.
3
Integrative Transcriptome and Epigenome Analysis of CN-AML
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Gene expression was obtained from published microarray data using Affymetrix Human Genome 133 plus 2.0 as well as U133A Gene Chips (accession number: GSE9476, GSE1159, GSE6891, GSE12417) (24 (link),25 (link),27 (link),28 (link)). Seventy-three CN-AML patients with mRNA, microRNA and methylation data were derived from The Cancer Genome Atlas (TCGA) (29 (link)). Design, data quality control and normalization of microarray experiments were in accordance with the standard Affymetrix protocols. Expression of mRNA and microRNA were obtained by high throughout transcriptome sequencing (RNA-seq), while methylation data was obtained by Illumina Infinium 450K BeadChips. The expression level of ANP32A was standardized in normally distributed. Then the appropriate cut-off subdivision value was compared by the 4 quartiles of 185 CN-AML patients, which the median value showed evident distinction (Figure S1A,B,C). Therefore, median value of ANP32A expression was used to classify patients into ANP32Ahigh and ANP32Alow groups. The expression levels of ERG, DNMT3A, BAALC, WT1 and other genes were obtained using the same strategy.
4
Microarray Analysis of FCER1G Expression
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All microarray data were identified in GEO, and we employed statistical analysis to investigate significantly abnormally expressed genes on every microarray dataset. Briefly, gene expression data were obtained by using Affymetrix human Genome 133 plus 2.0. All designs and quality control of the microarray experiment and data normalization were in line with the standard Affymetrix protocols. Patients with FCER1G expression values above the median for all MM patients were classified as FCER1Ghigh, and the others were considered to be FCER1Glow. P-value < 0.05 in unpaired t-test analysis and fold change (FC, log2) > 0.5 or < -0.5 was utilized to determine the differential expression of genes (DEGs).
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