Total RNA was amplified and reverse transcribed to cDNA using an Ambion WT Expression kit (Ambion), which was then fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix).(30 (link)) The resulting cDNA was then hybridized to a Human Gene Array 1.1 ST Array (Affymetrix) and subsequently washed and stained. Each step was carried out according to the manufacturer's protocol. The microarray gene chips were scanned using an AffyMetrix GeneChip Scanner 3000 and the normalized data were analyzed using GeneSpring software (Agilent). The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (31 (link)) and are accessible through GEO Series accession number GSE85582.
Genechip scanner 3000
Manufactured by Agilent Technologies
Sourced in United States
The GeneChip Scanner 3000 is a high-performance microarray scanner designed for the analysis of gene expression data. It is capable of detecting and quantifying fluorescent signals from DNA microarrays, enabling researchers to measure the expression levels of thousands of genes simultaneously.
Automatically generated - may contain errors
Lab products found in correlation
Mirna microarray 2, by Thermo Fisher Scientific (3 mentions)
Ambion wt expression kit, by Thermo Fisher Scientific (1 mentions)
Affymetrix genechip wt terminal labeling kit, by Thermo Fisher Scientific (1 mentions)
Genespring software, by Agilent Technologies (1 mentions)
Mirna complete labeling and hyb kit, by Agilent Technologies (1 mentions)
Spike in kit, by Agilent Technologies (1 mentions)
Omics explorer, by Qlucore (1 mentions)
Mirneasy kit, by Qiagen (1 mentions)
Agilent genespring gx, by Agilent Technologies (1 mentions)
Genespring gx software, by Agilent Technologies (1 mentions)
Agilent genespring gx software, by Agilent Technologies (1 mentions)
Thremo nanodrop 2000, by Agilent Technologies (1 mentions)
Genechip fluidics station 450, by Agilent Technologies (1 mentions)
Agilent rna 6000 nano kit, by Agilent Technologies (1 mentions)
Agilent 2100, by Agilent Technologies (1 mentions)
Genespring gx version 11, by Agilent Technologies (1 mentions)
U133plus2 microarrays, by Thermo Fisher Scientific (1 mentions)
Fluidics station, by Thermo Fisher Scientific (1 mentions)
7 protocols using genechip scanner 3000
1
Microarray Analysis of Total RNA
2
Microarray Analysis of miRNA Expression
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Total RNA was purified from cell lines using the miRNeasy kit (Qiagen, Valencia, CA, USA), and 100 ng was labeled and hybridized to the array using the miRNA complete labeling and hyb kit (Agilent, Santa Clara, CA, USA) and spike-in kit (Agilent). Data were generated on a GeneChip Scanner 3000 (Agilent), Human microRNA Microarray Release 16.0, 8x60K arrays (Agilent). Data were imported into R, RMA normalized using the package AgiMicroRna,46 (link) summarized to the log2 scale and returned for further association analysis as a gene by sample matrix. The miR expression data are MIAME compliant and have been submitted to the Gene Expression Omnibus (GSE73774). Differences in microRNA expression were determined with Omics Explorer (Qlucore, Lund, Sweden), using ANOVA on 549 miRs from TCGA12 (link) and 1368 miRs from cell lines using using a cutoff of P<0.05 and false discovery rate of 0.09 and 0.73, respectively, calculated using the Benjamini–Hochberg method. Fold change of miRs found to be significant (P<0.05) in both TCGA and cell lines was then determined by comparing expression in each cluster with the other two clusters (Table 3 ).
3
miRNA profiling in clear cell renal cell carcinoma
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MiRNA analysis was conducted using 9 ccRCC samples and matched-pair normal kidney samples on miRNA microarray 2.0 (Affymetrix, Santa Clara, CA, USA). The arrays were scanned using the Affymetrix Gene Chip Scanner 3000, and the scanned data were processed with the Agilent GeneSpring GX software (Agilent, Santa Clara, CA, USA) [18 ]. (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55138 ).
4
Urinary EV miRNA Profiling in Prostate Cancer
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Microarray analysis for miRNAs of EVs was performed with EVs isolated from urine obtained after DRE from 14 men with elevated PSA [negative (n=4) and PCa of Gleason score (GS) 6 (n=3), GS 7 (n=3), and GS 8–9 (n=4)] on miRNA microarray 2.0 (Affymetrix, Santa Clara, CA, USA). An Affymetrix Gene Chip Scanner 3000 was used to scan the arrays, after which GeneSpring GX software (Agilent, Santa Clara, CA, USA) was used to process the scanned data.
5
miRNA Profiling of Urinary and Tissue Samples in UC
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MiRNA analysis of EVs was conducted using urinary EVs from 6 UC patients and 3 HV on miRNA microarray 2.0 (Affymetrix, Santa Clara, CA, USA). MiRNA analysis of UC tissue specimens was conducted using 11 matched-pair samples (tumor and normal specimens) plus 10 tumor specimens on miRNA microarray 2.0 (Affymetrix) [32 (link)]. The arrays were scanned using the Affymetrix Gene Chip Scanner 3000, and the scanned data were processed with Agilent GeneSpring GX software (Agilent).
6
Transcriptome Analysis of Gene Expression
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The required reagents Agilent RNA 6000 Nano Kit, GeneChip 3’IVT Express Kit, GeneChip Hybridization Wash and Stain Kit, Trizol Kit, and QIAGEN RNeasy Total RNA Isolation kit were provided by Gekkai Gene Technology Co., Ltd. The main instruments used in the study included the Thremo Nanodrop 2000, Agilent 2100, GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450, and GeneChip Scanner 3000.
7
Gene Expression Profiling of RNA Samples
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3 µg of total RNA was used to generate double stranded cDNA. The cRNA was generated using either one- or two-cycle eukaryote target labelling along with controls supplied with the kit (Affymetrix, USA). The samples were biotin labelled and the cRNA randomly fragmented before hybridisation to Affymetrix U133plus2 microarrays following the manufacturer's instructions. The microarray chips were washed and stained using Affymetrix Fluidics Station and scanned using a GeneChip Scanner 3000.
Expression values were determined using Affymetrix Microarray Suite 5.0 and GeneSpring GX version 11.0 (Agilent Technologies, USA) was used for pre-processing the data using the MAS5 algorithm. All probe sets with absent flags were removed from the data. The data was baseline transformed to the median of all samples. Differentially expressed genes were detected using an unpaired t-test with unequal variance (Welch correction). P-values were corrected using a Benjamini-Hochberg adjustment for multiple testing. Probe sets having a P<0.05 and at least a two-fold change were considered to be differentially expressed. The microarray data is available from the GEO website (http://www.ncbi.nlm.nih.gov/geo/ ) with accession number GSE42806.
Expression values were determined using Affymetrix Microarray Suite 5.0 and GeneSpring GX version 11.0 (Agilent Technologies, USA) was used for pre-processing the data using the MAS5 algorithm. All probe sets with absent flags were removed from the data. The data was baseline transformed to the median of all samples. Differentially expressed genes were detected using an unpaired t-test with unequal variance (Welch correction). P-values were corrected using a Benjamini-Hochberg adjustment for multiple testing. Probe sets having a P<0.05 and at least a two-fold change were considered to be differentially expressed. The microarray data is available from the GEO website (
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