RNA was isolated from 15 paired normal and HNSCC tumor tissues (a subset of the total 33 paired tissues) and evaluated for quality and integrity (Bio-Rad Experion™ System) as done previously [Westbrook et al., 2014 (link)]. Whole genome transcript analysis was performed using Affymetrix 3000 7G System platform using Human GeneChip 1.0ST arrays. The Human GeneChip 1.0ST covers >30,000 coding transcripts, along with a small number of lincRNA transcripts. RNA samples were processed per manufacturers’ protocols using Ambion® Whole-Transcript (WT) Expression kit, and Affymetrix® GeneChip WT Terminal Labeling and Controls Reagent kit on Affymetrix equipment (Scanner 3000 7G System). Hybridized chips were automatically washed, stained and scanned at the UMMC Institutional Molecular and Genomics Core. Data obtained from these gene expression studies are deposited in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/ ) with the GEO accession number GSE58911.
Scanner 3000 7g system
Manufactured by Thermo Fisher Scientific
The Scanner 3000 7G System is a laboratory-grade scanner designed for high-performance imaging and analysis. It features a high-resolution, large-format scanning platform capable of capturing detailed images of various samples. The system is built with advanced optics and precision mechanisms to ensure accurate and repeatable scanning results.
Automatically generated - may contain errors
Lab products found in correlation
Experion system, by Bio-Rad (2 mentions)
Whole transcript expression kit, by Thermo Fisher Scientific (2 mentions)
3000 7g system platform, by Thermo Fisher Scientific (2 mentions)
Genechip wt terminal labeling and controls reagent kit, by Thermo Fisher Scientific (2 mentions)
Genechip 3 ivt plus reagent kit, by Thermo Fisher Scientific (1 mentions)
Fluidics station 450, by Thermo Fisher Scientific (1 mentions)
Genechip primeview human gene expression array, by Thermo Fisher Scientific (1 mentions)
3 protocols using scanner 3000 7g system
1
Whole Genome Transcriptome Analysis of HNSCC
2
Gene Expression Profiling of Pluripotent Cells
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Biotinylated cRNA was prepared from 100 ng of total RNA using a GeneChip 3'IVT PLUS Reagent kit (ThermoFisher Scientific, Waltham, MA) and was hybridized to the GeneChip PrimeView Human Gene Expression Array (ThermoFisher Scientific) for 16 hours at 45°C. Array slides were washed and stained in an Affymetrix Fluidics station 450, and scanned using a GeneChip scanner 3000 7G system. The data files were then uploaded to www.pluritest.org , scored for pluripotency, and deposited into the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database with accession no. GSE104605.
3
Whole Transcriptome Analysis of miRNA-Depleted Cells
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RNA was isolated from KHOS miROFF n-miR-G665 and KHOS miROFF Control cells and evaluated for quality and integrity (Bio-Rad Experion™ System). Whole genome transcript analysis was performed using Affymetrix 3000 7 G System platform using Human GeneChip 2.0ST arrays covering >30,000 coding transcripts. RNA samples were processed per manufacturers’ protocols using Ambion Whole-Transcript (WT) Expression kit, and Affymetrix GeneChip WT Terminal Labeling and Controls Reagent kit on Affymetrix equipment (Scanner 3000 7 G System). Hybridized chips processed at the UMMC Institutional Molecular and Genomics Core.
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