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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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Genetics 182, 133–144. A proximal centriole-like structure is present in Drosophila spermatids and can serve as a model to study centriole duplication. 2009

Blachon, S., Cai, X., Roberts, K.A., Yang, K., Polyanovsky, A., Church, A. and Avidor-Reiss, T.

Notes: These authors studied the formation of centrioles in Drosophila spermatids. Genomic DNA was extracted from whole flies using the Wizard® SV Genomic DNA Purification System. The DNA was then subjected to PCR, purified and sequenced. RNA was purified from whole flies using the SV Total RNA Isolation System. After RNA extraction, the samples were used in RT-PCR. (4064)

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J. Cell Sci. 121, 504–13. Integrin alpha9 beta1 is a receptor for nerve growth factor and other neurotrophins. 2008

Staniszewska, I., Sariyer, I.K., Lecht, S., Brown, M.C., Walsh, E.M., Tuszynski, G.P., Safak, M., Lazarovici, P. and Marcinkiewicz, C.

Notes: The authors investigated the ability of α9β1 integrin to act as a neurotrophin receptor and affect cell signaling pathways. As part of the study, RT-PCR was used to detect the presence of other neurotrophin receptors in their model cell line, SW480. Reverse transcription was performed using the Reverse Transcription System and 1µg of total RNA isolated using the SV Total RNA Isolation System. The resulting cDNA (5µg) was amplified for 35 cycles (β-actin as a control) or 40 cycles (TrkA and p75NTR) using GoTaq® Green Master Mix. RT-PCR results were confirmed by Western blot analysis. (3884)

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Eukaryot. Cell 7, 1965–1979. Transcriptome for photobiological hydrogen production induced by sulfur deprivation in the green alga Chlamydomonas reinhardtii. 2008

Nguyen, A.V., Thomas-Hall, S.R., Malnoë, A., Timmins, M., Mussgnug, J.H., Rupprecht, J., Kruse, O., Hankamer, B. and Schenk, P.M.

Notes: The authors analyzed the transcriptional activity of wild-type Chlamydomonas reinhardtii cultures sampled at different time points during the aerobic and anaerobic phase of the photobiological hydrogen production process under sulfur-depleted conditions. C. reinhardtii were grown in photobioreactors, carefully extracted, centrifuged and flash-frozen in liquid nitrogen. RNA was purified using the SV Total RNA Isolation System following the plant centrifugation protocol without sample grinding. The eluted RNA was quantitated and integrity checked by gel electrophoresis and qRT-PCR. Total RNA was used to synthesize labeled cDNA using the ChipShot™ Indirect Labeling and Clean-Up System. The labeled cDNA was used for probing microarrays. (4022)

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Brain Res. 1127, 66–75. Molecular characterization and gene expression of the pituitary adenylate cyclase-activating polypeptide (PACAP) in the lizard brain. 2007

Valiante, S., Prisco, M., Capaldo, A., Zambrano, I., De Falco, M., Andreuccetti, P., Laforgia, V., and Varano, L.

Notes: The authors cloned pituitary adenylate cyclase-activating polypeptide (PACAP) from lizard (Podarcis sicula) brain. They then isolated total RNA from lizard brain using the SV Total RNA Isolation System and used 4µg of total RNA in a reverse transcription with ImProm-II™ Reverse Transcriptase and oligo(dT)15 primers at 37°C for 1.5 hours. The PACAP cDNA was amplified by PCR, and the resulting PCR products were cleaned up using the Wizard® SV Gel and PCR Clean-Up System prior to sequencing. (3666)

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J. Leukoc. Biol. 79, 202–13. Induction of intracellular calcium elevation by {Delta}9-tetrahydrocannabinol in T cells involves TRPC1 channels. 2006

Rao, G.K. and Kaminski, N.E.

Notes: The authors studied the relationship between transient receptor potential canonical (TRPC) channels and Ca2+ elevation in the cannabinoid-2 receptor-expressing human peripheral blood-acute lymphoid leukemia (HPB-ALL) human T cell line. Total RNA from HPB-ALL cells was subjected to RT-PCR and the bands for TRPC1 were excised from a 1.2% NuSieve 3:1 agarose gel, purified using the Wizard® PCR Preps DNA Purification System and sequenced. Using 20nM synthesized siRNA specific for TRPC1 and a nonsilencing control sequence, 2.5 × 105 HPB-ALL cells/ml (a human T cell line) were transiently transfected for 48 hours using the CodeBreaker™ siRNA Transfection Reagent. After this 48-hour incubation, the siRNA-treated cells were either used for calcium determination or harvested and washed, and the RNA was isolated using the SV Total RNA Isolation System. The RNA was used for quantitative real-time PCR. (3316)

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Microbiology 150, 2037-2053. A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. 2004

Kelly, A., Goldberg, M.D., Carroll, R.K., Danino, V., Hinton, J.C.D. and Dorman, C.J.

Notes: These authors describe use of the SV Total RNA Isolation System to isolate total RNA from the bacterium Salmonella enterica serovar Typhimurium. The isolated RNA was used to make fluorescently labeled targets in a reverse transcription reaction. The labeled targets were used to analyze gene expression on microarrays. (3124)

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Infect. Immun. 72(2), 629–36. A K+ uptake protein, TrkA, is required for serum, protamine, and polymyxin B resistance in Vibrio vulnificus. 2004

Chen Y.C., Chuang Y.C., Chang C.C., Jeang C.L. and Chang M.C.

Notes: The authors identified a gene, trkA, in Vibrio vulnificus that is responsible for serum resistance and characterized this gene by genetic analysis. Total RNA was isolated from wild-type V. vulnificus CKM-1 using the SV Total RNA Isolation System. Subsequently, 0.1 µg RNA was used in a two-step RT-PCR to amplify three regions of interest both in trkA and downstream of trkA. The products were analyzed on a 2% agarose gel stained with ethidium bromide. (3072)

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Plant Physiol. 126, 1416–1429. Efficient prenylation by a plant geranylgeranyltransferase-I requires a functional CaaL box motif and a proximal polybasic domain. 2004

Caldelari, D., Sternberg, H., Rodríguez-Concepción, M., Gruissem, W. and Yalovsky, S.

Notes: Using the SV Total RNA Isolation System before RT-PCR, expression levels of AtGGT-IB were compared in flowers, leaves, stems, and root tissues of wildtype and era1-2 Arabidopsis plants. First-strand synthesis was performed with M-MLV Reverse Transcriptase using 500ng of RNA and an equal amount of oligo(dT). A 1:10 dilution of this product was used for amplification. (2855)

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J. Microbiol. Methods 58(1), 139–42. Improved method for the isolation of RNA from (standing liquid cultures of) Streptomycetes. 2004

Van Keulen G., Siebring J., Rembacz K.P., Hoogeveen M., Tomczynska M. and Dijkhuizen L.

Notes: These authors describe a new, quick method of isolating RNA from Streptomycetes coelicolor using five-day-old standing liquid cultures. They report higher yield, better quality RNA and increased purity compared to other methods. S. coelicolor spores were pregerminated, inoculated in liquid media and incubated at 30°C for five days. After incubation, the biomass from six 10 × 10 cm dishes was harvested by scraping the bottom of the dishes and filtering onto a membrane. Then the Mycelium was scraped from the membrane, transferred to a 1.5 ml vial, frozen in liquid nitrogen, and crushed by mortar and pestle. The resulting powder was then transferred to a tube containing 1ml Trizol, processed to extract RNA and the aqueous phase transferred to a new tube for DNase I treatment. Then 375µl of SV RNA dilution buffer was added to the nucleic acid solution, mixed and centrifuged. The resulting supernatant was mixed with 250µl cold 96% ethanol, loaded on an SV column and centrifuged for one minute. The column was then processed as described in the SV Total RNA Isolation System protocol. RNA was eluted from the column by adding 50µl of nuclease-free water and the concentration determined by spectrophotometry. To check the RNA quality, 5µg of the isolated RNA was loaded on a denaturing formaldehyde agarose gel and subjected to electrophoresis for 1 hour or used for Northern hybridizations with a nylon membrane. The 16S DNA probe was labeled with 32P-dCTP using the Prime-a-Gene® Labeling System. (3070)

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J. Exp. Bot. 353, 2125–6. RS2: a sugar beet gene related to the latex allergen Hev b 5 family. 2004

Fowler, M.R., Gartland, J., Norton, W., Slater, A., Elliott, M.C. and Scott N.W.

Notes: RNA was extracted from sugar beet (cv. Roberta) 14-day seedling, cotyledon, hypocotyl, 46-day plant, 90-day plant, petiole, leaf and root using the SV RNA Purification System. Twelve micrograms of RNA from each sample was used in a Northern blot analysis with a Psoralen-biotin probe. (2857)

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J. Biol. Chem. 279, 5249–56. The amitochondriate eukaryote Trichomonas vaginalis contains a divergent thioredoxin-linked peroxiredoxin antioxidant system. 2004

Coombs, G.H., Westrop, G.D., Suchan, P., Puzova, G., Hirt, R.P., Embley, T.M., Mottram, J.C., and Muller, S.

Notes: Total RNA was isolated from Trichomonas vaginalis G3 using the SV Total RNA Isolation System. The total RNA was used in 5´ RACE reactions to clone the ends of thioredoxin reductase gene TRX, TRXR, and TRXP mRNAs. (2853)

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J. Biol. Chem. 279, 39094-39104. The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing. 2004

Lou, X., Liu, Q., Tu, X., Wang, J., Teng, M., Niu, L., Schuller, D.J., Huang, Q. and Hao, Q.

Notes: In this study, the SV Total RNA Isolation System was used to isolate total RNA from venom sacs from Naja Atra (asian cobra). The Access RT-PCR System was used to reverse transcribe atratoxin and atratoxin-b cDNA from the isolated RNA. The amplified cDNAs were then cloned into the pGEM®-T vector. (3126)

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Antimicrob. Agents Chemother. 48(2), 484-490. The ybxI gene of Bacillus subtilis 168 encodes a class D beta-lactamase of low activity. 2004

Colombo M.L., Hanique S., Baurin S.L., Bauvois C., De Vriendt K., Van Beeumen J.J., Frere J.M. and Joris B.

Notes: The authors examined the ybxI gene in Bacillus subtilis 168 for beta-lactamase activity and penicillin recognition as the primary structure of YbxI was similar to that of beta lactamases. The SV Total RNA Isolation System was used to isolate RNA from an exponential growth phase B. subtilis 168 culture. To determine if yxbI was present in the harvested total RNA, the Access RT-PCR System was used to amplify the yxbI cDNA and the positive control B. subtilis yjbJ mRNA. The products were run on a 1% agarose gel and stained with ethidium bromide. (3073)

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Antimicrob. Agents Chemother. 47, 27–33. Contributions of MexAB-OprM and an EmrE homolog to intrinsic resistance of Pseudomonas aeruginosa to aminoglycosides and dyes 2003

Li X-Z., Poole K. and Nikaido H.

Notes: The authors examined the putative Pseudomonas aeruginosa homolog to the E. coli small multidrug resistance gene EmrE and its possible role in P. aeruginosa intrinsic drug resistance. Total RNA was isolated from 1-2ml log-phase or overnight stationary-phase P. aeruginosa PAO1 cultures grown in LB using the SV Total RNA Isolation System. After treating the RNA with DNase, 0.1µg RNA was used in the Access RT-PCR System to measure emrEPae expression and the constitutive rpsL gene. The two amplification products were then analyzed on a 1.7% agarose gel. (3074)

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Biochem. J. 373, 815–824. Extracellular ATP stimulates the early growth response protein 1 (Egr-1) via a protein kinase C-dependent pathway in the human osteoblastic HOBIT cell line. 2003

Pines, A., Romanello, M., Cestratto, L., Moro, G.L., D’Andrea, P., and Tell, G.

Notes: In this paper, the SV Total RNA Isolation System was used to isolate total RNA from human osteoblast HOBIT cells. One microgram of the purified DNA was used in RT-PCR with a 20mer oligo(dT) and gene-specific primers. (2850)

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Biochem. J. 371, 443-449. Identification by site-directed mutagenesis of amino acids contributing to ligand-binding specificity or signal transduction properties of the human FP prostanoid receptor. 2003

Neuschäfer-Rube, F., Engemaier, E., Koch, S., Böer U., and Püschel, G.P.

Notes: The SV Total RNA Isolation System was used to isolate total RNA from human placenta. The total RNA was used in RT-PCR to specifically amplify human FP prostanoid receptor 1 cDNAs. The amplified cDNAs were cloned and used in mutagenesis studies. (2852)

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Mol. Cell. Neurosci. 22, 383–395. Involvement of α7β1 integrin in the conditioning-lesion effect on sensory axon regeneration 2003

Ekström, P.A.R., Mayer, U., Panjwani, A., Pountney, D., Pizzey, J. and Tonge, D.A.

Notes: RNA was extracted from condition-lesioned and unoperated mouse thoracic dorsal root ganglion neurons, and cDNA was generated using Reverse Transcription System. Additionally, RNA was prepared from cut and unoperated mouse sciatic nerve samples using the SV Total RNA Isolation System. (2662)

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Clin. Can. Res. 9, 1393–1398. KAI1 metastasis suppressor protein is down-regulated during the progression of human endometrial cancer 2003

Liu, F-S., Dong, J-T., Chen, J-T., Hsieh, Y-T., Ho, E. S-C., Hung, M-J., Lu, C-H. and Chiou, L-C.

Notes: Total cellular RNA was isolated from fresh-frozen human endometrial specimens using the SV Total RNA Isolation System. (2651)

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J. Bacteriol. 185, 1153–1160. Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. Strain O-7. 2003

Orikoshi, H., Baba, N., Nakayama, S., Kashu, H., Miyamoto, K., Yasuda, M., Inamori, Y. and Tsujibo, H.

Notes: The SV Total RNA Isolation System was used to isolate total RNA from Alteromonas cultures. Five micrograms of the total RNA was used in reverse transcription reactions with M-MLV Reverse Transcriptase, RNase H Minus. cDNA chiB (chitinase B) products from the reaction were quantified by real-time PCR with SYBR green dye. (3023)

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J. Biol. Chem. 278 (35), 33384–33391. Role of the glucocorticoid receptor for regulation of hypoxia-dependent gene expression. 2003

Kodama, T., Shimizu, N., Yoshikawa, N., Makino, Y., Ouchida, R., Okamoto, K., Hisada, T., Nakamura, H., Morimoto, C. and Tanaka, H.

Notes: The SV Total RNA Isolation System was used to isolate total RNA from HeLa cells for RT-PCR analysis. Fifty nanograms of the total RNA was used as template in AccessQuick™ RT-PCR System reactions. VEGF, ADM, GLUT3, and β-actin mRNA levels in HeLa cells under normoxia and hypoxia conditions were analyzed. (2746)

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Proc. Natl. Acad. Sci. USA 100, 13773-13778. Shade is the Drosophila P450 enzyme that mediates the hydroxylation of ecdysone to the steroid insect molting hormone 20-hydroxyecdysone. 2003

Petryk, A., Warren, J.T., Marqués, G., Jarcho, M.P., Gilbert, L.I., Kahler, J., Parvy, J.P., Li, Y., Dauphin-Villemant, C. and O'Connor, M.B.,

Notes: Researchers used the SV Total RNA Isolation System to isolate total RNA from various tissues from Drosophila larvae. The isolated RNA from various tissues was used in reverse transcription reactions (using M-MLV Reverse Transcriptase) to make cDNAs of the shade (Shd) gene message. PCR amplification of Shd cDNA demonstrated that Shd was specifically expressed in certain Drosophila tissues. (2784)

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Mol. Pharmacol. 63(4), 915-924. Species-specific transcriptional activity of synthetic flavonoids in guinea pig and mouse cells as a result of differential activation of the aryl hydrocarbon receptor to interact with dioxin-responsive elements 2003

Zhou, J.G., Henry, E.C., Palermo, C.M., Dertinger, S.D. and Gasiewicz, T.A.

Notes: The species-specific response of mouse hepatoma (Hepa.2D) and guinea pig adenocarcinoma (GPC.16) cells to flavonoid treatment was explored in this study. Cell lines stably transfected with dioxin responsive element-driven luciferase constructs were treated with a series of flavanoids. Luciferase expression was measured using the Steady-Glo® Luciferase Assay sytem. To increase the number of cells available, cells were grown on Cytodex-1 beads in a larger volume, then split into an opaque 96-well plate prior to application of the Steady-Glo® Reagent. Total RNA was isolated using the SV Total RNA Isolation System, then used in real-time PCR to quantitate luciferase and GAPDH RNA levels after treatment. (3091)

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Appl. Environ. Microbiol. 69, 4648-4657. The mode of action of the Bacillus thuringiensis vegetative insecticidal protein Vip3A differs from that of Cry1Ab δ-endotoxin. 2003

Lee, M.K., Walters, F.S., Hart, H., Palekar, N., and Chen, J.S.

Notes: The SV Total RNA Isolation System was used to isolate total RNA from Tobacco Hornworn (M. Sexta) larvae. The RNA was reverse transcribed with primers specific to the δ-endotoxin-binding region from the cadherin ectodomain of BT-R1. (2785)

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J. Bacteriol. 184(21), 5880-5893. Yersinia enterocolitica type III secretion: yscM1 and yscM2 regulate yop gene expression by a posttranscriptional mechanism that targets the 5' untranslated region of yop mRNA. 2002

Cambronne, E.D. and Schneewind, O.

Notes: To analyze whether the presence or absence of calcium in Yersinia enterocolitica growth media affected secretion of Yersinia outer proteins (Yops), these researchers used mutational analysis on four gene products that work together to regulate yopQ expression. The various Y. enterocolitica strains were grown in TSB medium supplemented with 5mM CaCl2 or EGTA (+/-Ca2+). After a 2-hour incubation followed by a 2-hour induction, the cultures were centrifuged and the supernatant was separated from the cell pellet. After resuspension in cell lysis buffer, the pellet was subjected to French press and 100µl aliquots were used with the SV Total RNA Isolation System. The eluted total RNA was digested with DNase, phenol/chloroform extracted and ethanol precipitated. Once resuspended, 0.6µg of Yersinia RNA was used in two-step RT-PCR to amplify the yopQ gene and the amplimer was analyzed on an ethidium bromide-stained 2% agarose gel. (3071)

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