Quantigene viewrna probes

Manufactured by Thermo Fisher Scientific

Sourced in Canada

QuantiGene ViewRNA probes are a technology for sensitive and specific detection of RNA targets. They enable visualization of gene expression patterns in tissue samples. The probes are designed to hybridize to target RNA sequences and produce a signal that can be detected using specialized imaging equipment.

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Lab products found in correlation

Allprep dna rna ffpe kit, by Qiagen (1 mentions) Quantigene viewrna ish tissue assay kit, by Thermo Fisher Scientific (1 mentions) Axiovision software, by Zeiss (1 mentions) Axio imager a1 microscope, by Zeiss (1 mentions) Axiocam hrc camera, by Zeiss (1 mentions) Pre treatment solution, by Thermo Fisher Scientific (1 mentions)

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QuantiGene ViewRNA (8 citations) ViewRNA probes (2 citations)

4 protocols using quantigene viewrna probes

Single-Cell Gene Expression Analysis of FFPE Tissues

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RNA extracted from FFPE tissues (AllPrep DNA/RNA FFPE kit, Qiagen) and from lysed single cells were reverse transcribed and processed for Fluidigm Single Cell Gene Expression analysis as described (7 , 31 (link)). A brief pre-amplification of target transcripts was performed using a custom panel of 49 validated gene primer pairs (DELTAgene Assay, Fluidigm Corp.), followed by qPCR analysis on a BioMark HD Real-Time PCR System (Fluidigm Corp.). Dual color RNA-ISH of FFPE tissues was performed using custom designed QuantiGene ViewRNA probes (Affymetrix) against neural (ASCL1, GFAP, OLIG2, PDGFRA, and SOX2) and mesenchymal GBM subtype transcripts (SERPINE1, TGFB1, TGFBR2, and VIM) (see supplemental methods for a full description of these assays).

Sullivan J.P., Nahed B.V., Madden M.W., Oliveira S.M., Springer S., Bhere D., Chi A.S., Wakimoto H., Rothenberg S.M., Sequist L.V., Kapur R., Shah K., Iafrate A.J., Curry W.T., Loeffler J.S., Batchelor T.T., Louis D.N., Toner M., Maheswaran S, & Haber D.A. (2014). Brain Tumor Cells in Circulation are Enriched for Mesenchymal Gene Expression. Cancer discovery, 4(11), 1299-1309.

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In Situ Hybridization of Rat Kit Gene

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5 µm thick formalin-fixed, paraffin-embedded lung tissue sections were used for in situ hybridization with the QuantiGene ViewRNA ISH Tissue Assay kit (Affymetrix, Cleveland, OH) according to the manufacturer’s instructions. Custom TYPE1 QuantiGene View RNA probes were obtained from Affymetrix for rat Kit (Gen Bank Accession number NM_022264, region 501–1476 covered by probeset). Pretreatment was performed for 10 min at 95°C and protease digestion for 20 min at 40°C. TYPE1 probes were stained with Fast red and counterstained with Gill’s Hematoxylin. A negative control (probe omitted) was run in parallel (Figure S1). Images were taken with AXIO imager.A1 microscope, Axiocam HRc camera and Axiovision software (all Zeiss)

Farkas D., Kraskauskas D., Drake J.I., Alhussaini A.A., Kraskauskiene V., Bogaard H.J., Cool C.D., Voelkel N.F, & Farkas L. (2014). CXCR4 Inhibition Ameliorates Severe Obliterative Pulmonary Hypertension and Accumulation of C-Kit+ Cells in Rats. PLoS ONE, 9(2), e89810.

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Quantitative Lgr5+ Stem Cell Analysis

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Intestines from C57BL/6J mice were fixed overnight in 4% paraformaldehyde, embedded in paraffin, and cut in 5 μm sections. ISH was performed twice on 2 intestines each, using Quantigene ViewRNA probes (Affymetrix) for two-color ISH, as described in Supplemental Experimental Procedures. Between 320 and 460 Lgr5⁺ crypt base cells were counted in at least 50 crypts from each mouse (N=4). Cells were scored as DBL+ when at least one dot for a mature-cell marker mRNA (red) was present in a cell expressing Lgr5 mRNA (blue dots). Background signals were estimated from counts of red dots in 370 to 440 nucleated sub-epithelial cells for each mature-cell marker in each sample.

Kim T.H., Saadatpour A., Guo G., Saxena M., Cavazza A., Desai N., Jadhav U., Jiang L., Rivera M.N., Orkin S.H., Yuan G.C, & Shivdasani R.A. (2016). Single-cell transcript profiles reveal multilineage priming in early progenitors derived from Lgr5+ intestinal stem cells. Cell reports, 16(8), 2053-2060.

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Dual-colorimetric RNA-ISH for Epithelial and Mesenchymal Markers

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For quantiGene ViewRNA in-situ hybridization (ISH) on FFPE-tissue, a dual-colorimetric RNA-in situ hybridization (RNA-ISH) branched chain assay (Affymetrix Quantigene, Santa Clara, CA) was used to quantify multiple transcripts. 5-micron sections were fixed in 10% formaldehyde (Fisher Scientific, Pittsburgh, PA), deparaffinized, boiled in pre-treatment solution (Affymetrix, Santa Clara, CA) and digested with proteinase K. Sections were hybridized for 3 hours at 40°C with a cocktail of custom designed QuantiGene ViewRNA probes against epithelial (CDH1, EpCAM, KRT5, KRT7, KRT8, KRT18, KRT19; type 1 probes) and mesenchymal markers (FN1, CDH2, SERPINE1; type 6 probes) (Affymetrix, Santa Clara, CA). Bound probes were then amplified per protocol from Affymetrix using PreAmp and Amp molecules. Multiple Label Probe oligonucleotides conjugated to alkaline phosphatase (LP-AP Type 1) were then added and Fast Red Substrate was used to produce signal (red dots). For two color assays, an LP-AP type 6 probe was used with Fast Blue substrate (blue dots) followed by LP-AP type 1 probe with Fast Red Substrate (red dots) to produce dual colorimetric signals. Slides were then counterstained with Hematoxylin. Images were scanned by Aperio scanscope.

Javaid S., Zhang J., Smolen G.A., Yu M., Wittner B.S., Singh A., Arora K.S., Madden M.W., Desai R., Zubrowski M.J., Schott B.J., Ting D.T., Stott S.L., Toner M., Maheswaran S., Shioda T., Ramaswamy S, & Haber D.A. (2015). MAPK7 regulates EMT Features and Modulates the Generation of CTCs. Molecular cancer research : MCR, 13(5), 934-943.

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