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Appl. Environ. Microbiol. 78, 445–54. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. 2012

Ma, K., Conrad, R. and Lu, Y.

Notes: The authors of this study investigated the microbial mechanisms associated with the reduction of methane production and emission from rice fields observed with intermittent field drainage. They looked in particular at the abundance of mcrA gene copies and transcripts from rice paddy soil fauna. The mcrA gene encodes the alpha subunit of methyl coenzyme M reductase. 

Total nucleic acid was extracted from soil samples using a phenol-chloroform procedure. For RNA analyses, DNA was hydrolyzed using RQ1 RNase-free DNase in the presence of 0.2µl Recombinant RNasin® Ribonuclease Inhibitor and then further purified using a commercial kit. cDNA synthesis was carried out using the Improm-II™ Reverse Transcription System, again in the presence of 1.0µl Recombinant RNasin® Ribonuclease Inhibitor. A clone library of transcripts was generated using the pGEM®-T Easy Vector System. The transcript standard for quantitative mcrA analysis was prepared from the in vitro transcript of a mcrA clone using the Riboprobe® in vitro Transcription Systems. (4241)

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J. Neuroendocrinol. 19, 309-319. Inhibition of vasopressin V1b receptor translation by upstream open reading frames in the 5'-untranslated region. 2007

Rabadan-Diehl, C., Martínez, A., Volpi, S., Subburaju, S. and Aguilera, G.

Notes: The authors studied the rat VP V1b receptor (V1bR) gene including the 826 base 5´ UTR, which has five ORFs upstream (uORF) of the V1bR protein start codon, to examine the effect of the upstream peptides on V1bR translation. The V1bR gene was cloned into the pALTER®-MAX Vector, and substitution mutations were created in the uORF translation initiation codons with the Altered Sites® II in vitro Mutagenesis System. One microgram of the linearized pALTER®- V1bR construct was transcribed using the Riboprobe® System and translated using Wheat Germ Extract with or without 35S-methionine. The unlabeled protein was analyzed by Western blot. The radiolabeled protein was spun through a 3% sucrose cushion, precipitated and separated by SDS-PAGE. For a possible membrane-targeted protein, the uORF1 was transcribed in vitro and then translated using Rabbit Reticulocyte Lysate, Canine Pancreatic Microsomal Membanes and 35S-methionine. The proteins were spun through a 3% sucrose cushion and then run on a 15% SDS-PAGE gel to determine membrane presence. (3749)

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J. Biol. Chem. 282, 14413-144120.. Loss of HSulf-1 expression enhances autocrine signaling mediated by amphiregulin in breast cancer. 2007

Narita, K., Chien, J., Mullany, S.A., Staub, J., Qian, X., Lingle, W.L. and Shridhar, V.

Notes: These authors identified HSulf-1 as a downregulated gene in ovarian, breast and several other cancer cell lines. To investigate the clinical impact of this downregulation, tissue microarray was used look for associations between HSulf-1 expression levels and clinico-pathological parameters such as tumor histology, grade, hormone receptor status and presence of recurrent disease. HSulf-1 expression levels were determined by RNA in situ hybridization, using probes developed with the Riboprobe® System. (3616)

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J. Biol. Chem. 280, 28215-28220. Determination of the functionality of common APOA5 polymorphisms. 2005

Talmud, P.J., Palmen, J., Putt, W., Lins, L., and Humphries, S.E.

Notes: The authors investigated common variants of the APOA5 gene that have been associated with differences in plasma triglyceride (TG) levels. PCR fragments containing either the –1131T --> C promoter variant or containing both the –1131T --> C and –3G --> A promoter variants were cloned into the pGEM®-T Vector System. The fragments were subsequently cloned into the pGL3 Basic Vector and transiently transfected into Huh7 and HepG2 cells along with the luciferase control vector, pRL-TK. The cells were lysed 48 hours after transfection and Luciferase activity was measured with the Dual-Luciferase® Reporter Assay System. The function of the 1891T --> C variant in the 3´ UTR was tested the same way; with the exception that site-directed mutagenesis was performed to introduce the T --> C at position 1891 before the fragment was cloned into the pGL3 Basic Vector. The functionality of the Kozak sequence –3A --> G variant was determined by cloning cDNAs into the pGEM®-7Zf Vector. Transcription/translation experiments were performed using the TNT® Quick Coupled Transcription/Translation System and the proteins were labeled using the FluorTect™ GreenLys System. In addition, a primer extension inhibition assay was performed using capped mRNAs generated with the Riboprobe® System –T7 and the Ribo m7G Cap Analog. Ribosome binding reactions were performed using the Rabbit Reticulocyte Lysate System, Nuclease Treated. (3460)

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J. Biol. Chem. 280, 1376-1383. PDILT, a divergent testis-specific protein disulfide isomerase with a non-classical SXXC motif that engages in disulfide-dependent interactions in the endoplasmic reticulum. 2005

van Lith, M., Hartigan, N., Hatch, J. and Benham, A.M.

Notes: The tissue-specific patterns of expression of the novel protein disulfide isomerase-like protein of the testis (PDILT) was characterized using the AccessQuick™ RT-PCR System. RNAs isolated from various mouse tissues were amplified to reveal the testis-specific expression. An in vitro PDILT transcript generated using the Riboprobe® System-T7 was used as a positive control. Actin mRNA was also amplified to demonstrate equal RNA input. (3433)

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J. Biol. Chem. 278 (10), 8018-8027. Nuclear factor-κB and mitogen-activated protein kinases mediate nitric oxide-enhanced transcriptional expression of interferon-kβ. 2003

Jacobs, A.T. and Ignarro, L.J.

Notes: Promega T4 Polynucleotide Kinase was used to end-label an oligo representing a NF-kB binding sequence element with [γ-32P] ATP (7,000 Ci/mmol).  Specific primers to IFN-β and IκB-α messenger RNA were used in RT-PCR to generate products for cloning into the pGEM®-T Easy Vector. The resulting plasmids were linearized with Nco I and Spe I, respectively, and used as templates for in vitro transcription using the Riboprobe® System to generate probes for use in an RNase protection assay.  The antisense probes were labeled with [α-32P]CTP (800 Ci/mmol) in the Riboprobe® reactions.  RNase ONE™ Ribonuclease was also used in this study.  (3197)

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Proc. Natl. Acad. Sci. USA 99, 1443-1448. Stable suppression of gene expression by RNAi in mammalian cells. 2002

Paddison, P. J., Caudy, A. A., and Hannon, G. J.

Notes: Firefly and Renilla luciferase mRNA transcripts were synthesized with the Riboprobe® kit for use in in vitro translation and dicer experiments.  The Dual-Luciferase® Assay was used to analyze cotransfection experiments with the pRL-SV40 and pGL3-Control Vectors, and dsRNAs in P19 mouse embryonyl carcinoma cells. (2621)

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Plant Physiol. 127, 450-458. Control of specific gene expression by gibberellin and brassinosteroid. 2001

Bouquin, T., Meier, C., Foster, R., Nielsen, M.E., and Mundy, J.

Notes: Total RNA was isolated from Arabidopsis tissues using the RNAgents® Total RNA Isolation System. The RNA was further processed into the poly(A) fraction using the PolyATtract® mRNA Isolation System. The isolated RNA was used in Northern blot analysis. Blots were probed with a 32P-labeled RNA probe generated from a cDNA cloned into the pGEM®-T Easy Vector using the T7 Riboprobe® in vitro Transcription System. Bioluminescence from transgenic plants containing a firefly luciferase reporter was visualized by spraying the plants with a solution of 5mM Beetle Luciferin, Potassium Salt in 0.1% Triton® X-100. (2570)

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Genetics 154, 1485-1495. Regulation of the Yeast INO1 Gene. The products of the ino2, ino4 and opi1 regulatory genes are not required for repression in response to inositol. 2000

Graves, J. A. , Henry, S. A.

Notes: Linearized plasmid DNA templates were used in Riboprobe® in vitro Transcription Systems to produce RNA templates for in vitro translation using Rabbit Reticulocyte Lysate Systems, Nuclease Treated. (1117)

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Proc. Natl. Acad. Sci. USA 95, 9620-9625. Expression profiles of multiple genes in single neurons of Alzheimer's disease. 1999

Chow, N., Cox, C., Callahan, L.M., Weimer, J.M., Guo, L., Coleman, P.D.

Notes: RNA probes were generated with 35S-UTP using the Riboprobe® in vitro Transcription System. The labeled probes were used for in situ hybridization of 18µm sections of the hippocampus. (1298)

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J. Virol. 73, 2376-2384. Myxoma virus encodes an α2,3-sialyltransferase that enhances virulence. 1999

Jackson, R.J., Hall, D.F., Kerr, P.J.

Notes: The PolyATtract® System 1000 was used to isolate poly(A)+ RNA directly from myxoma virus-infected RK13 rabbit kidney cells. To obtain late viral RNAs, the RNA was isolated from the cells 16 hours after infection. For the early viral RNAs, the cells were treated with cycloheximide for 10 hours after infection prior to RNA isolation. The isolated RNA was used for Northern blot analysis with RNA probes prepared using the Riboprobe® System. (0966)

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J. Biol. Chem. 274, 28674-28681. Rat B2 sequences are induced in the hippocampal CA1 region after transient global cerebral ischemia. 1999

Liu, X., Clemens, J.A., Yin, T., Stephenson, D.T., Johnstone, E.M., Du, Y., Panetta. J.A., Paul, S.M., Little, S.P.

Notes: Total RNA was isolated from the CA1 dorsal hippocampus using the RNAgents® Total RNA Isolation System. The isolated RNA was used in differential display. One of the isolated clones was transcribed with the Riboprobe® in vitro Transcription System with 35S-UTP. The RNA probe was used for in situ hybridization. (0780)

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J. Biol. Chem. 273, 27474-27483. Sp1 and Sp3 regulate transcriptional activity of the facilitative glucose transporter isoform-3 gene in mammalian neuroblasts and trophoblasts. 1998

Rajakumar, R.A., Thamotharan, S., Menon, R.K., Devaskar, S.U.

Notes: AMV Reverse Transcriptase was used for primer extension analysis from poly(A)+ RNA. The Riboprobe® in vitro Transcription System was used to generate [32P]-antisense RNA probes for RNase protection assays. Promoter studies were performed in N2A murine neuroblasotoma cells. Experimental constructs were assembled in the pGL2-Basic Vector and cotransfected with the pRL-TK Vector at a 10:1 ratio and luciferase activities determined with the Dual-Luciferase® Reporter Assay System. Some promoter studies were performed in Drosophila Schneider cells with luciferase promoter constructs and an RSV-driven beta-galactosidase vector. Beta-Galactosidase activity was determined with the Beta-Galactosidase Enzyme Assay System. (0531)

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J. Biol. Chem. 273, 22091-22095. The a1(VIII) and a2(VIII) chains of type VIII collagen can form stable homotrimeric molecules. 1998

Illidge, C., Kielty, C., Shuttleworth, A.

Notes: The Flexi® Rabbit Reticulocyte Lysate System was used for cell-free translation reaction in the presence of 4 x 105 digitonin-permeabilized HT-1080 fibroblasts. Two types VIII chains were expressed as well as the a1chain of type X collagen. The expressed proteins were assayed by protease digestion and thermal denaturation for their quaternary structure. The in vitro transcripts for the translation reaction were produced with the Riboprobe® System. (0995)

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Am. J. Physiol. 274, E656-E664. The cAMP-response element mediates induction of secretogranin II by CHX and FSK in GH4C1 cells. 1998

Jones, L.C., Scammell, J.G.

Notes: Authors used the Wizard® Plus Megapreps DNA Purification System to isolate DNA and transfect it into GH cells. They also used the β-Galactosidase Enzyme Assay System and Riboprobe® in vitro Transcription Systems in their studies. (0945)

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J. Neurosci. 17, 5070-5079. A family of delayed rectifier Kv1 cDNAs showing cell type-specific expression in the squid stellate ganglion/giant fiber lobe complex. 1997

Rosenthal, J.J.C, Liu, T.I. and Gilly, W.F.

Notes: The Riboprobe® in vitro Transcription System was used to produce 32P-labeled RNA probes for RNase protection assays. The fmol® DNA Cycle Sequencing System was used to directly sequence PCR products with [33P]end-labeled primers. (1526)

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J. Neurosci. 17, 5843-5857. Caenorhabditis elegans levamisole resistance genes lev-1, unc-29 and unc-38 encode functional nicotinic acetylcholine receptor subunits. 1997

Fleming, J.T., Squire, M.D., Barnes, T.M., Tornoe, C., Matsuda, K., Ahnn, J., Fire, A., Sulston, J.E., Barnard, E.A., Sattelle, D.B. and Lewis, J.A.

Notes: The cDNAs of interest were in vitro transcribed with the system and microinjected into Xenopus laevis oocytes for translation. (1559)

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J. Neurosci. 17, 5629-5639. Calcium channel density and hippocampal cell death with age in long-term culture. 1997

Porter, N.M., Thibault, O., Thibault, V., CHen, K.-C. and Landfield, P.W.

Notes: The Riboprobe® in vitro Transcription System was used to produce 32P-labeled RNA probes for RNase protection assays. (1521)

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J. Neurosci. 17, 181-189. Conservation of topology, but not conformation, of the proteolipid proteins of the myelin sheath. 1997

Gow A., Gragerov A., Gard A., Colman D.R., Lazzarini R.A.

Notes: All cDNAs to be translated in vitro were subcloned into the pSP64 Poly(A) Vector. The vector was linearized and RNA transcribed from the SP6 promoter with the Riboprobe® in vitro Transcription System. The in vitro transcribed RNA was translated in the Rabbit Reticulocyte Lysate in the presence or absence of Canine Pancreatic Microsomal Membranes (CMMs). N-linked glycosylation sequences were engineered into the proteolipid protein to determine the orientation of the domains of the protein in the membrane. (1114)

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J. Neurosci. 17, 7288-7296. Disruption of a single allele of the nerve growth factor gene results in atrophy of basal forebrain cholinergic neurons and memory deficits. 1997

Chen, K.S., Nishimura, M.C., Armanini, M.P., Crowley, C., Spencer, S.D. and Phillips, H.S.

Notes: The system was used to produce 33P-labeled RNA probes for use in RNase protection assays. (1557)

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J. Neurosci. 17, 3455-3466. Glutamate, but not dopamine, stimulates stress-activated protein kinase and AP-1-mediated transcription in striatal neurons. 1997

Schwarzschild, M. A., Cole, R. L., Hyman, S. E.

Notes: The Riboprobe® in vitro Transcription System was used to produce RNA probes for Northern analysis. (0417)

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J. Neurosci. 17(10), 3455-3466. Glutamate, but not dopamine, stimulates stress-activated protein kinase and AP-1-mediated trascription in striatal neurons. 1997

Schwarzschild, M.A., Cole, R.L. and Hyman, S.E.

Notes: The Riboprobe in vitro Transcription System was used to produce RNA probes for Northern analysis. (2250)

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Proc. Natl. Acad. Sci. USA 94, 5273-5277. Molecular cloning, sequence, expression, and processing of the interleukin 16 precursor. 1997

Baier, M., Bannert, N., Werner, A., Lang, K. and Kurth, R.

Notes: To identify the true transcriptional start of the IL-16 mRNA methods for rapid amplification of cDNA ends were applied. The complete pro-IL-16 cDNA was cloned, sequenced, and expressed in COS-7 cells. The authors used the pGEM®-T Vector System to clone fragments that were then used as templates in the Riboprobe® in Vitro Transcription System. (1453)

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J. Neurosci. 17, 4121-4128. Neuritic outgrowth associated with astroglial phenotypic changes induced by antisense glial fibrillary acid protein (GFAP) mRNA in injured neuron-astrocyte cocultures. 1997

Lefrançois, T., Fages, C., Peschanski, M. and Tardy, M.

Notes: The Riboprobe in vitro Transcription System was used to produce antisense RNA for liposome-mediated transfection into the neuron-astrocyte cocultures. (1567)

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J. Neurosci. 17, 9095-9103. Phosphodiesterase I, A Novel Adhesion Molecule and/or Cytokine Involved in Oligodendrocyte Function. 1997

Fuss, B. , Baba, H. , Phan, T. , Tuohy, V. K. , Macklin, W. B.

Notes: The Riboprobe® in vitro Transcription System (T7) was used to generate 32P-labeled probes for use in RNase protection assays. (1133)

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