Cyanine 5 ctp

Manufactured by PerkinElmer

Sourced in United States, Canada

Cyanine 5-CTP is a fluorescent dye used in a variety of scientific applications. It is a cyanine dye that can be used to label nucleic acids, proteins, and other biological molecules. The core function of Cyanine 5-CTP is to provide a fluorescent signal that can be detected and measured in various analytical techniques.

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Lab products found in correlation

Cyanine 3 ctp, by PerkinElmer (3 mentions) Nd 1000 spectrophotometer, by Thermo Fisher Scientific (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Quick amp labeling kit, by Agilent Technologies (1 mentions) Nanodrop one spectrophotometer, by Thermo Fisher Scientific (1 mentions) Agilent dna microarray scanner, by Agilent Technologies (1 mentions)

Spelling variants of this product

Cyanine 5 (11 citations) Cyanine 3- or 5-labeled CTP (4 citations)

3 protocols using cyanine 5 ctp

Mouse Spleen RNA Profiling Protocol

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Equal amounts of RNA prepared from individual spleen tissues of three mice were pooled. Labeling was performed as detailed in the protocol for the One-Color Microarray-Based Gene Expression Analysis (version 5.5, part number G4140-90050). Briefly, 1 μg of total RNA was used for amplification and labeling using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP and cyanine 5-CTP (PerkinElmer, Waltham, MA, USA). Yields of complementary RNA (cRNA) and the dye-incorporation rate were measured with the ND-1000 spectrophotometer (NanoDrop Technologies).

Dkhil M.A., Lubbad M.Y., Al-Shaebi E.M., Delic D, & Al-Quraishy S. (2015). The antiplasmodial and spleen protective role of crude Indigofera oblongifolia leaf extract traditionally used in the treatment of malaria in Saudi Arabia. Drug Design, Development and Therapy, 9, 6235-6246.

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Bulk mRNA Expression Analysis for HER2-targeted Therapy

Cited 3 times

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Bulk mRNA expression analysis was performed as described elsewhere^{21 (link)}. Briefly, RNA was extracted using the RNeasy Mini Kit (QIAGEN) and quantified by the NanoDrop One spectrophotometer (Thermo Fisher Scientific). RNA samples were labeled with cyanine 5-CTP or cyanine 3-CTP (PerkinElmer) using the Quick Amp Labeling Kit (Agilent Technologies). The gene expression microarray experiments were performed by comparing each baseline sample to samples taken after 14–21 d of HER2-targeted therapy (on-treatment). Each on-treatment sample was compared to the pre-treatment sample from the same patient. Limma v.3.28.21 (refs. ^{46 (link),47 (link)}) was used for background correction (‘normexp’), within-array normalization (‘loess’), between-array normalization and for averaging over replicate probes. For the downstream analyses, including batch correction and comparisons with the DSP cohort, the normalized counts were converted to log₂space. Combat^{48 (link)} was used to remove potential batch affects associated with microarray run date. PAM50 status pre-treatment and on-treatment was inferred using absolute intrinsic molecular subtyping, an n-of-1 algorithm that is robust to variations in dataset composition^{49 (link)}. This approach was utilized given the expected preponderance of HER2-enriched cases in this cohort.

McNamara K.L., Caswell-Jin J.L., Joshi R., Ma Z., Kotler E., Bean G.R., Kriner M., Zhou Z., Hoang M., Beechem J., Zoeller J., Press M.F., Slamon D.J., Hurvitz S.A, & Curtis C. (2021). Spatial proteomic characterization of HER2-positive breast tumors through neoadjuvant therapy predicts response. Nature cancer, 2(4), 400-413.

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Microarray Profiling of Brain and Breast Tissues

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RNA from 35 BBM, 10 non-neoplastic brain (NBn) and 10 non-neoplastic breast (NBr) tissues were profiled using Agilent whole human genome 4×44K mRNA expression microarrays. A quick-amplification kit (Agilent Technologies) was used to amplify and label 500 ng target mRNA species into complementary RNA (cRNA) for oligo microarrays according to the manufacturer's protocol. For each two-color array, a commercial universal reference RNA (Stratagene, La Jolla, CA) was labeled with cyanine 5-CTP and cyanine-3-CTP (Perkin Elmer, Boston, MA). Complimentary RNA concentration and labeling efficiency were measured spectrophotometrically. Approximately 800 ng of both Cy5-labeled experimental cRNA and Cy3-labeled universal reference RNA were hybridized to each microarray (adjusting for labeling efficiency). Images were captured using an Agilent DNA microarray scanner set at default settings for gene expression. Scanned images were processed using Feature Extractor v. 10.5.1.1software by applying a LOWESS (locally weighted linear regression) correction for dye bias and background noise was subtracted from spot intensities. To filter the preprocessed data, genes with a background signal higher than feature signal were removed.

Salhia B., Kiefer J., Ross J.T., Metapally R., Martinez R.A., Johnson K.N., DiPerna D.M., Paquette K.M., Jung S., Nasser S., Wallstrom G., Tembe W., Baker A., Carpten J., Resau J., Ryken T., Sibenaller Z., Petricoin E.F., Liotta L.A., Ramanathan R.K., Berens M.E, & Tran N.L. (2014). Integrated Genomic and Epigenomic Analysis of Breast Cancer Brain Metastasis. PLoS ONE, 9(1), e85448.

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