3 ivt express labeling kit

Manufactured by Thermo Fisher Scientific

The 3' IVT Express Labeling Kit is a laboratory tool designed for the efficient and rapid labeling of RNA samples. It provides a streamlined workflow for generating labeled RNA, which can be used in various downstream applications such as gene expression analysis and RNA-based assays.

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Lab products found in correlation

Trizol, by Thermo Fisher Scientific (2 mentions) Nanodrop 1000, by Thermo Fisher Scientific (2 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions) Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions) Genechip scanner 7g, by Thermo Fisher Scientific (1 mentions) Fs 450 fluidics station, by Thermo Fisher Scientific (1 mentions)

4 protocols using 3 ivt express labeling kit

Transcriptomic analysis of ECM/Fibronectin response

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After 48 hours on ECM or fibronectin (FN), RNA was harvested using E.Z.N.A Total RNA Kit (Omega) and analyzed on a nanodrop 1000 (Thermo Scientific) and Bioanalyzer 2100 (Agilent Technologies) for quality control. RNA samples were then amplified converted to cDNA, labeled using 3’ IVT Express Labeling Kit (#901229), and hybridized on an Affymetrix PrimeView Human Array Chip. The chip was scanned on an Affymetrix GeneChp 7G scanner. Raw intensity scores were imported into Partek Genomics Suite 6.6 (6.13.0731) and normalized on a gene level using the standard Robust Multi-array Average (RMA) algorithm for normalization and background correction. A two-way ANOVA was set up and a step-up FDR corrected P-value was included for every P-value calculated. Only significant gene changes with a P-value of ≤0.05 and a fold change greater than 1.5 were uploaded into MetaCore™ for pathway and gene otology analysis.

Scherzer M.T., Waigel S., Donninger H., Arumugam V., Zacharias W., Clark G., Siskind L.J., Soucy P, & Beverly L. (2015). Fibroblast-Derived Extracellular Matrices: An Alternative Cell Culture System That Increases Metastatic Cellular Properties. PLoS ONE, 10(9), e0138065.

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Profiling Molecular Subtypes of Medulloblastoma

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RNA was extracted from 29 frozen MB using Trizol (Invitrogen, Carlsbad, CA) and profiled by AROS Biosciences on the Affymetrix human genome U133 Plus 2.0 array with the 3′ IVT Express Labeling Kit (Affymetrix, Santa Clara, CA). Relative mean expression levels for each gene were calculated by the Affymetric microarray software. CEL files were preprocessed using RMA and probeset collapsed to genes using the Genepattern software suite (www.broadinstitute.org/cancer/software/genepattern/) [22 (link)]. Samples were then assigned to molecular subgroups as previously described, using a classifier based on support-vector machines [23 (link)].

McKinney N., Yuan L., Zhang H., Liu J., Cho Y.J., Rushing E., Schniederjan M, & MacDonald T.J. (2014). EphrinB1 expression is dysregulated and promotes oncogenic signaling in medulloblastoma. Journal of neuro-oncology, 121(1), 109-118.

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Microarray-based Molecular Subtyping of Samples

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mRNA extracted from MB samples using Trizol (Invitrogen, Carlsbad, CA) was profiled by AROS Biosciences on the Affymetrix human genome U133 Plus 2.0 array with the 3' IVT Express Labeling Kit (Affymetrix, Santa Clara, CA). CEL files were preprocessed using RMA [24 (link)] and probesets collapsed to genes using the Genepattern software suite (www.broadinstitute.org/cancer/software/genepattern/). Samples were assigned to molecular subgroups as previously described, using a classifier based on support-vector machines [25 (link)]. The relative mean expression level for each gene is calculated by the Affymetrix software.

Petersen W., Liu J., Yuan L., Zhang H., Schneiderjan M., Cho Y.J, & MacDonald T.J. (2014). Dasatinib suppression of medulloblastoma survival and migration is markedly enhanced by combining treatment with the aurora kinase inhibitor AT9283. Cancer letters, 354(1), 68-76.

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Differential Gene Expression Analysis of WT and TKO MEFs

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In triplicate, 100 ng of total RNA from either WT or TKO MEFs was amplified and labeled following the Affymetrix (Santa Clara, CA) standard protocol for their 3’IVT Express Labeling Kit, followed by hybridization to Affymetrix MOE430 2.0 Expression arrays. The arrays were processed following the manufacturer recommended wash and stain protocol on an Affymetrix FS-450 fluidics station and scanned on an Affymetrix GeneChip^® 7G scanner using Command Console 3.1. The resulting.cel files were imported into Partek Genomics Suite 6.5 and transcripts were normalized and summarized using RMA as normalization and background correction method. Contrasts in a 1-way ANOVA were set up to compare the groups of interest. FDR was chosen as multiple test correction for the resulting p-values.

Kruer T.L., Dougherty S.M., Reynolds L., Long E., de Silva T., Lockwood W.W, & Clem B.F. (2016). Expression of the lncRNA Maternally Expressed Gene 3 (MEG3) Contributes to the Control of Lung Cancer Cell Proliferation by the Rb Pathway. PLoS ONE, 11(11), e0166363.

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