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Genes Immun. 15, 33-7. A comprehensive analysis of the binding of anti-KIR antibodies to activating KIRs. 2014

Czaja, K., Borer, A.-S., Schmied, L., Terszowski, G., Stern, M., and Gonzalez, A.

Notes: Peripheral blood mononuclear cells were labeled with antibodies and sorted. Each sorted subset was immediately processed for total RNA with the ReliaPrep™ RNA Cell Miniprep System. The RNA was converted to cDNA then analyzed for expression level of three targets by qPCR with the dye-based GoTaq® qPCR System. (4600)

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PLos ONE 9, e106190. Anoctamin-1 in the juvenile rat urinary bladder. 2014

Bijos, D.A., Drake, M.J., and Vahabi, B.

Notes: Total RNA was extracted from mucosa and denuded-detrusor layers of rat bladders with the ReliaPrep™ RNA Tissue Miniprep System and converted to cDNA using GoScript™ Reverse Transcription System prior to PCR amplification. (4608)

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Toxicol. Rep. 1, 589-95. Arsenic (+3 oxidation state) methyltransferase is a specific but replaceable factor against arsenic toxicity. 2014

Tokumoto, M., Kutsukake, N., Yamanishi, E., Katsuta, D., Anan, Y., and Ogra, Y.

Notes: Total RNA was isolated from untreated HepG2 cells to clone the AS3MT transcript by RT-PCR, and for RT-qPCR analysis following AS3MT-directed siRNA treatment. The total RNA was isolated with the ReliaPrep™ RNA Cell Miniprep System. The health of the siRNA-treated cells was monitored with the CellTiter 96® AQueous One Solution Cell Proliferation Assay. (4620)

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Eur. J. Nutr. 53, 1051–1064. Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia 2014

Bogovič, B. M., Obermjer, T., Lipoglavšek, L, Grabnar, I., Avguštin, G. and Rogelj, I.

Notes: The authors of this study used real time-qPCR and PCR-DGGE (denaturing gradient gel electrophoresis) to analyze and compare the mixed bacterial systems from fecal samples of vegetarians and omnivores. Bacterial DNA was isolated from frozen fecal samples using the Maxwell® 16 Tissue DNA Purification Kit, and PCR-DGGE reactions were set up using GoTaq® Flexi DNA Polymerase and GoTaq® Flexi Colorless Reaction Buffer. The authors of this study were able to detect differences in microbiota that seemed to be related to diet. (4523)

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Mol. Cell. Biol. 34, 3486–99. Cellular migration and invasion uncoupled: Increased migration is not an inexorable consequence of epithelial-to-mesenchymal transition. 2014

Schaeffer, D., Somarelli, J.A., Hanna, G. and Palmer, G.M.

Notes: Rat renal DT and A3 cells were examined for differences in EGFR expression by RT-qPCR. Total RNA was isolated with the ReliaPrep™ RNA Cell Miniprep System and reverse transcribed with the GoScript™ Reverse Transcription System followed by dye-based qPCR analysis. (4617)

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PLos ONE 9, e104566. Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics 2014

Heydt, C., Fassunke, J., Künstlinger, H., Ihle, M.A., König, K., Heukamp, L.C., Schidhaus, H-U., Odenthal, M., Büttner, R. and Merkelbach-Bruse, S.

Notes: The authors of this study set out to compare five automated systems for purification of DNA from FFPE tissue samples and five DNA quantification methods to determine the systems and methods most favorable to successful downstream massively parallel sequencing (next generation sequencing) analysis. Tissues were processed using commercially available DNA purification kits available for each platform. The authors concluded that the DNA extracted using the Maxwell® 16 systems and platform was of the highest quality in this study and gave the best results in downstream applications. (4512)

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Methods 67, 36–44. Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates 2014

Schapire, A.L., Bologna, N.G., Moro, B., Zhai, J., Meyers, B.C. and Palatnik, J.F.

Notes: The authors of this study present a method for genome-wide analysis of miRNA processing intermediates in plants. The method presented uses reverse transcription performed with a mix of primers designed against known miRNA precursors. The molecules are next amplified to generate a library for deep sequencing. Total RNA was isolated and purified from plant tissue and then treated with RQ1 RNase-Free DNase to remove contaminating DNA. Ribosomal RNA was selectively removed before adapter ligation and reverse transcription. cDNA libraries were prepared; PCR products from the libraries were separated on an agarose gel and purified using Wizard® SV Gel and PCR Clean-Up System prior to sequencing. (4561)

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Forensic Sci. Int. Genet. 13, 195–205. Developmental validation of the PowerPlex® ESI 16/17 Fast and PowerPlex®ESX 16/17 Fast Systems. 2014

McLaren, R.S., Bourdeau-Heller, J., Patel, J., Thompson, J.M., Pagram, J., Loake, T., Beesley, D., Pirttimaa, M., Hill, C.R., Duewer, D.L., Kline, M.C., Butler, J.M. and Storts, D.R.

Notes:   (5201)

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PLos ONE 9, e107236. Familly with sequence similarity 5, member C (FAM5C) increases leukocyte adhesion molecules in vascular endothelial cells: Implication in vascular inflammation. 2014

Sato, J., Kinugasa, M., Satomi-Kobayashi, S., Hatakeyama, K., Knox, A.J., Asada, Y., Wierman, M.E., Hirata, K., and Rikitake, Y.

Notes: Human Umbillical Vein Endothelial Cells (HUVECs) were transfected with FAM5C or mock transfected and tested for changes in specific gene expression and changes associated with TNFα treatment. RNA was isolated with the ReliaPrep™ RNA Cell Miniprep System prior to RT-qPCR with a dye-based system. Mice were also treated with TNFα and expression levels were examined for specific targets using total RNA isolated from brain and aorta using the ReliaPrep™ RNA Tissue Miniprep System followed by dye-based RT-qPCR. (4597)

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Mol. Metab. 3, 731-41. Fractalkine (CX3CL1), a new factor protecting β-cells against TNFα. 2014

Rutti, S., Arous, C., Schvartz, D., Timper, K., Sanchez, J.-C., Dermitzakis, E., Donath, M.Y., Halban, P.A., and Bousakri, K.

Notes: Human pancreas islet cells were isolated by cell sorting and total RNA was isolated from 100 islet equivalents using the ReliaPrep™ RNA Cell Miniprep System. The RNA was analyzed by probe-based RT-qPCR. (4622)

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Mol. Pharmacol. 85, 83–90. Identification of novel functionally selective κ-opioid receptor scaffolds. 2014

White, K.L., Scopton, A.P., Rives, M.L., Bikbulatov, R.V., Polepally, P.R., Brown, P.J., Kenakin, T., Javitch, J.A., Zjawiony, J.K. and Roth, B.L.

Notes: The authors were interested in testing selective agonists of the κ-opioid receptor (KOR)-dynorphin with a bias for G proteins. Human embryonic kidney cells were transfected with a 1:1 ratio of a plasmid encoding KOR and the pGloSensor™-22F cAMP Plasmid. The transfected cells were plated into a 384-well plate the next day and treated with test compound for 20–30 minutes. Then GloSensor™ cAMP Reagent and isoproterenol were added, incubated for 10 minutes and Gai-mediated activity was assessed by measuring luminescence. (4520)

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PLos ONE 9, e98877. Induction of cell-mediated immune responses in mice by DNA vaccines that express hepatitis C virus NS3 mutants lacking serine protease and NTPase/RNA helicase activities. 2014

Ratnoglik, S.L., Jiang, D.-P., Aoki, C., Sudarmono, P., Shoji, I., Deng, L. and Hotta, H.

Notes: Primary splenocytes were isolated from mice immunized with an NS3 expression vector and examined for IFN-γ expression by RT-qPCR. Total RNA was isolated with the ReliaPrep™ RNA Cell Miniprep System and converted to cDNA with the GoScript™ Reverse Transcription System. The affect of wildtype and mutant NS3 on interferon-β promoter activity with an IFN-β promoter firefly luciferase vector and pRL-TK vector control was measured with the Dual-Luciferase® Reporter Assay System. LDH release was measured with the CytoTox 96® Cytotoxicity Assay in a cytotoxic T-lymphocyte assay using cultured splenocytes from the immunized mice. (4609)

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Fitoterapia. 99, 276–83. Inhibition of hepatitus C virus replication by chalepin and pseudane IX isolated from Ruta angustifolia leaves. 2014

Wahyuni, T.S., Widyawaruyanti, A., Lusida, M.I., Fuad, A., Soetjipto, Fuchino, H., Kawahara, N., Hayashi, Y., Aoki, C. and Hotta, H.

Notes: Huh7.5 cells were infected with HCV and treated with the plant-derived chemicals. The expression of viral messages was analyzed by RT-qPCR. Total RNA was isolated with the ReliaPrep™ RNA Cell Miniprep System and reverse transcribed with the GoScript™ Reverse Transcription System before dye-based qPCR analysis. (4616)

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J. Proteome Res. 13, 5041–50. Large-scale label-free comparative proteomics analysis of polo-like kinase 1 inhibition via the small-molecule inhibitor BI 6727 (Volasertib) in BRAFV600E mutant melanoma cells. 2014

Cholewa, B.D., Pellitteri-Hahn, M.C., Scarlett, C.O. and Ahmad, N.

Notes: Cell pellets of A375 human melanoma cells were lysed by passing through a needle, centrifuged to remove debris and protein quantitated. Twenty micrograms of protein from control and treated lysates were digested with 1µg of Sequencing Grade Modified Trypsin and used for mass spectrometry analysis. A375 cells (5 × 105) were grown in a 10cm dish and treated for 24 hours before isolating RNA and DNA synthesized using M-MLV Reverse Transcriptase. The cDNA was then used in qPCR. A375 cells were plated at 3 × 103 in 96-well half-volume white-wall plates, grown and treated for 24 hours. NAD, NADH and NADPH were determined using the NAD(P)H-Glo™ Detection System or NAD/NADH-Glo™ Assay and luminescence measured. (4963)

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Hum. Mol. Genet. 23, 209-25. Loss of FHL1 induces an age-dependent skeletal muscle myopathy associated with myfibrillar and intermyofibrillar disorganization in mice 2014

Domenighetti, A. A. et al. 

Notes: Expression of FHL1 mRNA (four-and-a-half LIM domain protein 1) was studied. Total RNA was isolated from mutant and wildtype mouse skeletal muscle, and then first-strand cDNA synthesis carried out using the GoTaq® 2-Step RT-qPCR System. (4559)

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Cardiovasc Res. 103, 607–18. Mechanisms underlying capsaicin effects in canine coronary artery: implications for coronary spasm. 2014

Hiett, S.C., Owen, M.K., Li, W., Chen, X., Riley, A., Noblet, J., Flores, S., Sturek, M., Tune, J.D. and Obukhov, A.G.

Notes: Total RNA was isolated from freshly collected, snap-frozen canine coronary arteries using the ReliaPrep™ RNA Tissue Miniprep System and used for semi-quantitative RT-PCR with limited cycle numbers. (4614)

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EMBO J. 33, 1565-1581. MiR-133 promotes cardiac reprogramming by directly repressing Snai1 and silencing fibroblast signatures 2014

Muraoka, N., Yamakawa, H., Miyamoto, K., Sadahiro, T., Umei, T., Isomi, M., Nakashima, H., Akiyama, M., Wada, R., Inagawa, K., Nishiyama, T., Kaneda, R., Fukuda, T., Takeda, S., Tohyama, S., Hashimoto, H., Kawamura, Y., Goshima, N., Aeba, R., Yamagishi, H., Fukuda, K. and Ieda, M.

Notes: For construction of the Snai1 30 UTR reporter, the CMV promoter was subcloned into the promoterless pGL3-Basic vector upstream of the luciferase gene. A 755-bp Snai1 30 UTR fragment containing miR-133a-binding sites was amplified by PCR and subcloned into the modified pGL3-Basic vector. The activities of firefly luciferase and renilla luciferase in the control vector were determined by the Dual-Glo® Luciferase Assay System. RNA was extracted from MEFs, GMT-, GMT/miR-133-, or GMT/miR-133/ Snai1-induced aMHC-GFP+ cells, neonatal mouse heart tissues, HCFs, GMTMM-, GMTMM/miR-133-, GMTMM/miR-133/Snai1-transduced HCFs using ReliaPrep™ RNA Cell Miniprep System for gene microarray analysis. (4737)

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PLos ONE 9, e106575. Platform comparison for evaluation of ALK protein immunohistochemical expression, genomic copy number and hotspot mutation status in neuroblastomas. 2014

Yan, B., Kuick, C.H., Lim, M., Venkataraman, K., Tennakoon, C., Loh, E., Lian, D., Leong, M.Y., Lakshmanan, M., Tergaonkar, V., Sung, W.K., Soh, S.Y. and Chang, K.T.

Notes: The authors isolated genomic DNA from neuroblastoma FFPE samples using the ReliaPrep™ FFPE gDNA Miniprep System followed by PCR enrichment and NGS on an Ion PGM™ System. (4913)

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Mol. Pharmacol. 85, 472–81. Regulation of beta-2-adrenergic receptor function by conformationally selective single-domain intrabodies. 2014

Staus, D.P. et al.

Notes: The authors screened a panel of monomeric single-domain antibodies (nanobodies; Nbs) that recognize the G protein-coupled β2 adrenergic receptor (β2AR) to characterize the antibodies' ability to stabilize the active or inactive receptor conformations. They expressed these Nbs intracellularly (as "intrabodies") in HEK293 cells and measured intracellular cAMP levels as an indication of β2AR activity. cAMP levels were determined using the GloSensor™ cAMP biosensor, a genetically modified form of firefly luciferase into which a cAMP-binding protein moiety is inserted such that cAMP binding induces a conformational change and leads to increased light output. (4516)

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Biochem. Biophys. Res. Commun. 446, 30-6. Reversine increases the plasticity of lineage-committed preadipocytes to osteogenesis by inhibiting adipogenesis through induction of TGF-β pathway in vitro. 2014

Park, J.G., Lee, D.-H., Moon, Y.S., and Kim, K.-H.

Notes: 3T3-L1 preadipocytes were treated with various levels of reversine and monitored for induction of apoptosis with the Caspase-Glo® 3/7 Assay with data collected on a GloMax® Instrument. Changes in gene expression of three targets upon reversine treatment were examined through total RNA isolation with the ReliaPrep™ RNA Cell Miniprep System, reverse transcription with the ImProm-II™ Reverse Transcription System followed by dye-based qPCR analysis. (4596)

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Acta Biomater. 10, 3177-87. Three-dimensional hydrogel scaffolds facilitate in vitro self-renewal of human skin-derived precursors. 2014

Wang, X., Liu, S., Zhao, Q., Li, N., Zhang, H., Zhang, X., Lei, X., Zhao, H., Deng, Z., Qiao, J., Cao, Y., Ning, L., Liu, S., and Duan, E.

Notes: Human Skin Progenitor (HSK) cells were cultured on hydrogels and either left alone or differentiated into various skin cell types. Gene expression changes were monitored by isolating total RNA from collagenase and hyaluronidase treated hydrogels with the ReliaPrep™ RNA Cell Miniprep System followed by cDNA synthesis with the GoScript™ Reverse Transcription System and qPCR with the dye-based GoTaq® qPCR System. (4602)

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FASEB J. 28, 946–55. Transcriptional control of the B3GALT5 gene by a retroviral promoter and methylation of distant regulatory elements. 2014

Zulueta, A., Caretti, A., Signorelli, P., Dall'olio, F. and Trinchera, M.

Notes: RNA was isolated from several cell lines using the SV Total RNA Isolation System and ReliaPrep™ RNA Cell Miniprep System. RNA was used in competitive RT-PCR to characterize splice variants of the B3GALT5 long terminal repeat, HNFα and HNFβ1. (4445)

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J. Biol. Chem. 288, 34470-83. Chemotype-selective modes of action of κ-opioid receptor agonists. 2013

Vardy E., Mosier P.D.,  Frankowski K.J., Wu H., Katritch, V., Westkaemper R.B., Aubé, J., Stevens R.C., Roth B.L.

Notes: The authors sought to determine whether different residues had specific roles in binding and activation of the k-opioid receptor (KOR) by agonist molecules with distinct chemotypes. For function assays they introduced point mutations into human KOR using site-directed mutagenesis. All mutations were verified by Sanger automated sequencing. HEK293T cells were cotransfected with pGloSensor™-22F cAMP Plasmid plus the different KOR variants. Cells were plated, and after 24 hours, medium replaced with drug buffer and the different drug treatments. cAMP production was detected by treatment with isoproterenol in GloSensor™ Reagent. (4519)

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ACS Chemical Biology 8, 1018–26. Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. 2013

Weiss, D.R. et al.

Notes: The authors investigated the utility of virtual screening to identify agonists for the active form of the G protein-coupled β2 adrenergic receptor (β2AR). During screening, they maintained the active form of β2AR with conformationally selective antibodies and used cAMP levels to quantify β2AR activity. cAMP levels were determined using the GloSensor™ cAMP biosensor, a genetically modified form of firefly luciferase into which a cAMP-binding protein moiety is inserted such that cAMP binding induces a conformational change and leads to increased light output. (4517)

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Methods 6, 283–291. Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. 2013

Schapire, A.L., Bologna, N.G., Moro, B., Zhai, J., Meyers, B.C. and Palatnik, J.F.

Notes: The authors developed a complete method for making cDNA libraries containing miRNA processing-intermediates that used the RQ1 RNase-Free DNase and Wizard® SV Gel and PCR Clean-Up System. (4920)

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