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Quantigene viewrna ish tissue assay kit

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The QuantiGene ViewRNA ISH Tissue Assay Kit is a tool used for the detection and visualization of RNA molecules in fixed tissue samples. It enables the localization and quantification of specific RNA targets within the cellular context.

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Lab products found in correlation

Viewrna probe sets, by Thermo Fisher Scientific (3 mentions) Eclipse te2000 u microscope, by Nikon (2 mentions) Quantigene viewrna ish cell assay kit, by Thermo Fisher Scientific (2 mentions) Bz 9000, by Keyence (1 mentions) Ab9574, by Abcam (1 mentions) 3 3 diaminobenzidine tetrahydrochloride, by Vector Laboratories (1 mentions) Envision system hrp, by Agilent Technologies (1 mentions) Tsa plus dig kit, by PerkinElmer (1 mentions) Target retrieval solution, by Agilent Technologies (1 mentions) Tsc sp8 confocal microscope, by Leica (1 mentions) Confocal microscope, by Zeiss (1 mentions) Hoechst 33342 dye, by Thermo Fisher Scientific (1 mentions) Sp8 confocal microscope, by Leica (1 mentions) Quantigene viewrna probes, 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) Type 6 primary probes, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

ViewRNA ISH tissue assay (10 citations) QuantiGene ViewRNA (8 citations) ISH kit (6 citations) QuantiGene® ViewRNA ISH Tissue Assay (5 citations) QuantiGene ViewRNA assay (5 citations) QuantiGene ViewRNA ISH Tissue Kit (3 citations)

17 protocols using quantigene viewrna ish tissue assay kit

1

TRIM9 Expression Analysis in Tumor Tissues

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The QuantiGene®ViewRNA ISH Tissue Assay kit (Affymetrix, Santa Clara, CA, USA) was used according to the manufacturer’s protocol. FFPE Sections (4 μm) of tumor tissues were incubated at 98 °C with a pretreatment solution for 20 min, followed by protease digestion for 10 min. The TRIM9-specific View RNA™ Probe set (Affymetrix) was hybridized for 2 h. A TRIM9 specific probe set was then designed to hybridize the common sequence of TRIM9_v1 and TRIM9_v2 (1319 bp). ISH images were obtained under fluorescent microscopy (BZ9000; Keyence, Osaka, Japan). Signal intensity was semi-quantitatively determined based on the number of cytoplasmic fluorescent dots in five non-overlapping fields at high-power magnification (×400).
Formalin-fixed paraffin Sections (3 μm) of the tumor tissues were obtained for immunohistochemical staining with rabbit anti-TRIM9 polyclonal antibody (ProteinTech Group, Inc., Chicago, IL, USA) at a dilution of 1:400 according to a previously described method for ER, PR and Ki-67, with a slight modification in that antigen retrieval was accomplished by incubating at 98 °C in citrate buffer (pH 9.0) for 40 min (Shimomura et al. 2009 (link); Tanei et al. 2009 (link)). Immunohistochemical staining for TRIM9 was classified as 3+ (strongly positive), 2+ (intermediately positive), 1+ (weakly positive) or 0 (negative). The sections were counterstained with hematoxylin.
Mishima C., Kagara N., Matsui S., Tanei T., Naoi Y., Shimoda M., Shimomura A., Shimazu K., Kim S.J, & Noguchi S. (2015). Promoter methylation of TRIM9 as a marker for detection of circulating tumor DNA in breast cancer patients. SpringerPlus, 4, 635.
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2

Immunohistochemical Analysis of Liver Markers

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The livers were fixed in phosphate-buffered 10% formalin for 24 h, and paraffin sections were then prepared. Immunohistochemical staining was carried out with the EnVision/HRP system (Dako, Carpinteria, CA, USA) on deparaffinized sections treated with Target Retrieval Solution (Dako). The antibodies used were as follows: anti-insulin-like growth factor 2 (IGF2) (ab9574; Abcam, Cambridge, UK), anti-α-fetoprotein (AFP) (14550-1-AP, for mouse tissues; Proteintech Group, Chicago, IL, USA), anti-AFP (A0008, for human tissues; Dako), and anti-trefoil factor 3 (TFF3) (Abbiotec, San Diego, CA, USA). 3,3′-Diaminobenzidine tetrahydrochloride (Vector Laboratories, Burlingame, CA, USA) was used for signal detection. For the detection of the TFF3 peptide, we applied signal amplification using the TSA Plus DIG Kit (PerkinElmer, Waltham, MA, USA). In situ hybridization for non-coding H19 mRNA was carried out on deparaffinized sections using the mouse H19 QuantiGene ViewRNA Probe Set (VB6-16706; Affymetrix, Santa Clara, CA, USA) and the QuantiGene ViewRNA ISH Tissue Assay Kit (Affymetrix).
Chen X., Yamamoto M., Fujii K., Nagahama Y., Ooshio T., Xin B., Okada Y., Furukawa H, & Nishikawa Y. (2015). Differential reactivation of fetal/neonatal genes in mouse liver tumors induced in cirrhotic and non-cirrhotic conditions. Cancer Science, 106(8), 972-981.
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3

RNA Visualization in Tissue Sections

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RNA was visualized in paraffin-embedded sections using the QuantiGene ViewRNA ISH Tissue Assay Kit (Affymetrix, Frederick, MD, USA). In brief, tissue sections were rehydrated and incubated with proteinase K. Subsequently, they were incubated with ViewRNA probe sets designed against human TUG1, miR-145 and Notch1 (Affymetrix).
Katsushima K., Natsume A., Ohka F., Shinjo K., Hatanaka A., Ichimura N., Sato S., Takahashi S., Kimura H., Totoki Y., Shibata T., Naito M., Kim H.J., Miyata K., Kataoka K, & Kondo Y. (2016). Targeting the Notch-regulated non-coding RNA TUG1 for glioma treatment. Nature Communications, 7, 13616.
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4

Dual-color RNA-FISH for HBB and UBC

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RNA-FISH was performed using QuantiGene® ViewRNA ISH Tissue Assay kit, according to the manufacturer's protocols (Affymetrix). Tissue sections (4 µm) were deparaffinized, fixed in 4% phosphate-buffered paraformaldehyde, boiled in pre-treatment solution, and digested with proteinase K (included in kit). Sections were hybridized for three hours at 40°C with a probe designed against the human HBB and ubiquitin-C (UBC) (Affymetrix). Hybridized probes were then amplified using PreAmp and Amp molecules. Multiple Label Probe oligonucleotides conjugated to alkaline phosphatase (LP-AP, included in kit) were then added and FastRed (for HBB) or FastBlue (for UBC) substrates were used to produce fluorescent signals. Nuclei were then counterstained with DAPI. As for fluorescent imaging and processing, a series of high-resolution monochromatic images were captured using an automated microscope platform equipped with 60× objective magnification (PM-2000TM; HistoRx). Fluorescent filters (DAPI, Cy3, and Cy5) were used to detect dual-color RNA-FISH signals within each section. Images were depicted by pseudo-color merging using the image processing software ImageJ (National Institutes of Health, USA). HBB signals (Cy3) were colored red and UBC signals (Cy5) were green; nuclei were colored blue (DAPI).
Minami H., Isomoto H., Nakayama T., Hayashi T., Yamaguchi N., Matsushima K., Akazawa Y., Ohnita K., Takeshima F., Inoue H, & Nakao K. (2014). Background Coloration of Squamous Epithelium in Esophago-Pharyngeal Squamous Cell Carcinoma: What Causes the Color Change?. PLoS ONE, 9(1), e85553.
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5

RNA Visualization in Tissue Sections

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RNA was visualized in paraffin-embedded tissue sections using the QuantiGene ViewRNA ISH Tissue Assay Kit (Affymetrix, Frederick, MD, USA). In brief, tissue sections were rehydrated and incubated with proteinase K. Subsequently, they were incubated with ViewRNA probe sets designed to target human SPRIGHTLY and MYC (Affymetrix, Santa Clara, CA, USA). Custom Type 1 primary probes targeting SPRIGHTLY and Type 6 primary probes targeting MYC were designed and synthesized by Affymetrix (Santa Clara, CA, USA; Supplementary File 1). Hybridization was performed according to the manufacturer’s instructions.
Lee B., Katsushima K., Pokhrel R., Yuan M., Stapleton S., Jallo G., Wechsler-Reya R.J., Eberhart C.G., Ray A, & Perera R.J. (2022). The long non-coding RNA SPRIGHTLY and its binding partner PTBP1 regulate exon 5 skipping of SMYD3 transcripts in group 4 medulloblastomas. Neuro-Oncology Advances, 4(1), vdac120.
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6

In Situ Detection of Prg4 Transcripts

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Detection of Prg4 transcripts on cryotome sections (7 µm) was conducted using QuantiGene®® ViewRNA ISH Tissue Assay Kit and QuantiGene®® ViewRNA ISH Cell Assay Kit (Affymetrix, Santa Clara, CA, USA) according to the instruction of the manufacturer. An Alexa Fluor 488 (Affymetrix, USA) labeled probe targeting nucleotides 2721–3891 of the murine transcript variant 1 (NM_021400.3,) was used to detect PRG4 expression in situ. Stained sections were analyzed by immunofluorescence microscopy (Nikon Eclipse TE2000-U Microscope, Nikon, Tokyo, Japan).
Georgieva V.S., Etich J., Bluhm B., Zhu M., Frie C., Wilson R., Zaucke F., Bateman J, & Brachvogel B. (2020). Ablation of the miRNA Cluster 24 Has Profound Effects on Extracellular Matrix Protein Abundance in Cartilage. International Journal of Molecular Sciences, 21(11), 4112.
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7

Visualizing HCV RNA in Liver Tissue

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Formalin fixed liver sections were prepared as per immunohistochemical staining and stained using the Quantigene ViewRNA ISH tissue assay kit (QVT0012, Affymetrix) and co-stained with anti-HSA (ab2406, ab19180 Abcam) antibodies according to the manufacturer’s instructions. Two type 6 probe sets specific for HCV RNA (VF6-18614, VF6-11508) were used in this study. Images were captured using an Olympus upright confocal microscope.
Zheng Z., Sze C.W., Keng C.T., Al-Haddawi M., Liu M., Tan S.Y., Kwek H.L., Her Z., Chan X.Y., Barnwal B., Loh E., Chang K.T., Tan T.C., Tan Y.J, & Chen Q. (2017). Hepatitis C virus mediated chronic inflammation and tumorigenesis in the humanised immune system and liver mouse model. PLoS ONE, 12(9), e0184127.
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8

Visualizing RNA Transcripts in Tissue

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RNA transcripts were visualized in OCT-embedded tissue sections using the QuantiGene ViewRNA ISH tissue assay kit (Affymetrix, Santa Clara, CA). The assay was performed according to the tissue-based ViewRNA assay protocol with formaldehyde fixation and a 20-min protease treatment. ViewRNA probes were detected at 650 nm using a Leica TSC SP8 confocal microscope at 40× magnification.
Martinek J., Lin J., Kim K.I., Wang V.G., Wu T.C., Chiorazzi M., Boruchov H., Gulati A., Seeniraj S., Sun L., Marches F., Robson P., Rongvaux A., Flavell R.A., George J., Chuang J.H., Banchereau J, & Palucka K. (2022). Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function. Cell Reports Medicine, 3(5), 100621.
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9

Quantitative RNA Localization in Tissue

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A QuantiGene @ ViewRNA ISH Tissue Assay Kit (Affymetrix, USA) was used for RNA hybridization according to the kit instructions. Briefly, RORB and NRIP2 were used as TYPE1 probes, and GAPDH was used as a control probe. After staining the nucleus with DAPI or Hoechst 33342 dye (Invitrogen, Carlsbad, CA), the distribution and expression of RORB and NRIP2 were observed under a confocal microscope (Carl Zeiss Jena, Germany).
Wen Z., Pan T., Yang S., Liu J., Tao H., Zhao Y., Xu D., Shao W., Wu J., Liu X., Wang Y., Mao J, & Zhu Y. (2017). Up-regulated NRIP2 in colorectal cancer initiating cells modulates the Wnt pathway by targeting RORβ. Molecular Cancer, 16, 20.
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10

Spatial Expression Analysis of Collagen and Cathepsin K

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Transcripts were detected on frozen sections of femora (7 µm, n = 4 biological replicates per genotype) isolated from male newborn Cre and hKO mice as described previously16 (link) using the QuantiGene ViewRNA ISH Tissue Assay Kit and QuantiGene ViewRNA ISH Cell Assay Kit (Affymetrix, USA) according to the manufacturer’s instructions. Alexa Fluor 488 labeled probes (Affymetrix, USA) were used to detect Col1a1 (NM_007742.3) and Ctsk (NM_007802.4) expression in situ. Sections were analyzed by immunofluorescence microscopy (Nikon Eclipse TE2000-U Microscope, Nikon, Tokyo, Japan). For quantification, the Ctsk+ pixels per mm2 was determined.
Georgieva V.S., Bluhm B., Probst K., Zhu M., Heilig J., Niehoff A, & Brachvogel B. (2022). Ablation of the miRNA cluster 24 in cartilage and osteoblasts impairs bone remodeling. Scientific Reports, 12, 9116.
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