Management and visualization of whole genome shotgun assemblies using SAM.

abstract：:Real-time PCR is becoming a preferred method for quantification of minute amounts of nucleic acids. To achieve the full potential of this technique, accurate and convenient models for post-PCR data analysis are required. In this study, three different models were chosen to quantify the definitive copy numbers of Cucum...

journal_title：BioTechniques

authors： Feng J,Zeng R,Chen J

更新日期：2008-06-01 00:00:00

abstract：:Gel retardation analysis, or band shift assay, is technically the simplest method to investigate protein-nucleic acid interactions. In this report, we describe a nonradioactive band shift assay using a fluorescent DNA target and an ALFexpress automatic DNA sequencer in place of the current method that utilizes radioac...

journal_title：BioTechniques

authors： Filée P,Delmarcelle M,Thamm I,Joris B

更新日期：2001-05-01 00:00:00

abstract：:We report a robust method for studying en masse changes in translation using cDNA arrays. The relative distribution of messenger RNAs (mRNAs) along polysome gradients was monitored by performing cDNA array analysis of each gradient fraction and quantifying the mRNA translational status by regression analysis. Using th...

journal_title：BioTechniques

authors： Mazan-Mamczarz K,Kawai T,Martindale JL,Gorospe M

更新日期：2005-07-01 00:00:00

abstract：:Antibodies specific to avian myeloblastosis virus envelope glycoprotein gp80 were raised. Immunoliposomes were prepared using anti-avian myeloblastosis virus envelope glycoprotein gp80 antibody. The antibody was palmitoylated to facilitate its incorporation into lipid bilayers of liposomes. The fluorescence emission s...

journal_title：BioTechniques

authors： Kalvakolanu DV,Abraham A

更新日期：1991-08-01 00:00:00

abstract：:Plasmid DNA can be purified in 20 min using a three-step CsCl gradient in a vertical tube rotor. Ultracentrifugation with discontinuous gradients yields DNA with purity comparable to that obtained with longer isopycnic separations and with columns. ...

journal_title：BioTechniques

authors： Dorin M,Bornecque CA

更新日期：1995-01-01 00:00:00

abstract：:At many research institutions, lab space is more valuable than gold. Developers are taking note by designing smaller instruments with enhanced capabilities. Nathan Blow looks inside today's tiny lab. ...

journal_title：BioTechniques

authors： Blow NS Ph D

更新日期：2017-01-01 00:00:00

abstract：:A simple, non-destructive procedure is described to determine the quality of DNA arrays before they are used. It consists of a preliminary staining step of the DNA microarray by using SYBR green II, a fluorophore with specific affinity for ssDNA, followed by a laser scan analysis. The surface quality, integrity and ho...

journal_title：BioTechniques

authors： Battaglia C,Salani G,Consolandi C,Bernardi LR,De Bellis G

更新日期：2000-07-01 00:00:00

abstract：:Oligonucleotide primers used to amplify target DNA regions via PCR should meet certain design criteria to maximize the potential for efficient priming. The Random Oligonucleotide Construction Kit (ROCK), a spreadsheet-based program that runs under Microsoft Excel 97 or later version for Microsoft Windows, was develope...

journal_title：BioTechniques

authors： Strain SR,Chmielewski JG

更新日期：2001-06-01 00:00:00

abstract：:We have developed an automated purification method for dye-terminator-based DNA sequencing products using a magnetic bead approach. This 384-well protocol generates sequence fragments that are essentially free of template DNA, salt, and excess dye-terminator products. In comparison with traditional ethanol precipitati...

journal_title：BioTechniques

authors： Elkin C,Kapur H,Smith T,Humphries D,Pollard M,Hammon N,Hawkins T

更新日期：2002-06-01 00:00:00

abstract：:We report a modification of a liquid hybridization method that serves as a rapid, sensitive alternative to Southern hybridization for the analysis of polymerase chain reaction (PCR) products. An aliquot of the completed PCR is mixed with an internally nested, end-labeled oligonucleotide probe, and one cycle of PCR is ...

journal_title：BioTechniques

authors： Parker JD,Burmer GC

更新日期：1991-01-01 00:00:00

abstract：:Hematopoietic stem cells (HSCs) express Mdr1a/1b and Bcrp1/Abcg2, which are members of the ATP binding cassette transporter family. Mice lacking both Mdr1-type genes (Mdr1a and Mdr1b) or Bcrp1 had normal hematopoietic development, but it has been unclear whether Mdr1a/1b and Bcrp1 play redundant roles in hematopoiesis...

journal_title：BioTechniques

authors： Zhou S,Zong Y,Lu T,Sorrentino BP

更新日期：2003-12-01 00:00:00

abstract：:Screening methods for chemotherapeutic agents usually rely on the cytotoxic properties of the drugs. However, agents that inhibit invasion may have more efficacy and cause fewer side effects. Various cellular invasion assays have been used to evaluate these types of compounds, including the modified Boyden chamber, mo...

journal_title：BioTechniques

authors： Sasaki CY,Passaniti A

更新日期：1998-06-01 00:00:00

abstract：:We have generated a genomic P1 bacteriophage library using Monterey pine (Pinus radiata) DNA. We first developed a method for isolating from pine tissue the very high molecular weight DNA necessary for the preparation of libraries requiring large inserts. The method involves protoplasting the cells, isolating nuclei a...

journal_title：BioTechniques

authors： Gorman SW,Roberts-Oehlschlager SL,Cullis CA,Teasdale RD

更新日期：1992-05-01 00:00:00

abstract：:An improved method was developed for in situ reverse transcription-polymerase chain reaction (RT-PCR) to detect and localize mRNA in tissue sections. The coverslip mounted-immersion cycled (COSMIC) in situ RT-PCR technique combines the advantages of solution-phase PCR with the tissue immobilization necessary for in si...

journal_title：BioTechniques

authors： Ertsey R,Scavo LM

更新日期：1998-01-01 00:00:00

abstract：:We have demonstrated that efficient polymerase chain reaction amplifications from chromosomal DNA can be carried out using whole bacterial cells as the starting material. Cells from the liquid or solid cultures can be used directly, without any pre-treatment, thus eliminating the need for DNA isolation. ...

journal_title：BioTechniques

authors： Joshi AK,Baichwal V,Ames GF

更新日期：1991-01-01 00:00:00

abstract：:The green fluorescent protein (GFP) from the jellyfish Aequorea victoria is rapidly becoming an important reporter molecule for monitoring gene expression and protein localization in vivo, in situ and in real time. GFP emits bright green light (lambda max = 509 nm) when excited with UV or blue light (lambda max = 395 ...

journal_title：BioTechniques

authors： Kain SR,Adams M,Kondepudi A,Yang TT,Ward WW,Kitts P

更新日期：1995-10-01 00:00:00

abstract：:An assay is described in which an oligonucleotide probe is specifically digested by lambda exonuclease only when it is annealed to its complementary sequence. In this assay, a cycling effect occurs whereby a small amount of target sequence acts as a specific co-factor in the enzymatic degradation of a larger number of...

journal_title：BioTechniques

authors： Copley CG,Boot C

更新日期：1992-12-01 00:00:00

abstract：:Currently, in real-time PCR, one often has to choose between using a sequence-specific probe and a nonspecific double-stranded DNA (dsDNA) binding dye for the detection of amplified DNA products. The sequence-specific probe has the advantage that it only detects the targeted product, while the nonspecific dye has the ...

journal_title：BioTechniques

authors： Lind K,Ståhlberg A,Zoric N,Kubista M

更新日期：2006-03-01 00:00:00

abstract：:In this communication we describe the sequential use of standard and low-melting agarose in a single gel slab for the electrophoresis of DNA. This method has the advantages of high resolution and reproducibility characteristic of standard agarose and the ease of manipulation of DNA for direct cloning, sequential diges...

journal_title：BioTechniques

authors： Fotadar U,Shapiro LE,Surks MI

更新日期：1991-02-01 00:00:00

abstract：:A new qualitative PCR product detection assay called competitive amplified single mutation detection by selective probe hybridization immunoassay (CASSI) was developed for genotyping the most common apolipoprotein E (apoE) polymorphisms. Single target DNA strands immobilized using biotin on streptavidin-coated micropl...

journal_title：BioTechniques

authors： Köhler T,Rost AK,Purschwitz K,Vondran S,Remke H,Wagner O,Richter V

更新日期：1998-07-01 00:00:00

abstract：:Drosophila provides a powerful experimental system to analyze gene functions in a multi-cellular organism. Here we describe an in vivo method that interferes with the integrity of selected proteins through site-specific cleavage in Drosophila. The technique is based on the highly specific seven-amino-acid recognition ...

journal_title：BioTechniques

authors： Harder B,Schomburg A,Pflanz R,Küstner K,Gerlach N,Schuh R

更新日期：2008-05-01 00:00:00

abstract：:We observed the presence of contaminating NADH oxidation activity in maltose binding protein (MBP) fusion proteins expressed in Escherichia coli and purified using conventional amylose resin-based affinity chromatography. This contaminating NADH oxidation activity was detectable with at least four different enzymes fr...

journal_title：BioTechniques

authors： Guo F,Zhu G

更新日期：2012-04-01 00:00:00

abstract：:For a feasible and cost-effective impedance measurement of cellular alterations in real-time, we combined commercially available microelectrode arrays (MEAs), consisting of 60 microelectrodes, with a conventional impedance analyzer. For proof of principle, a breast carcinoma cell line (MCF-7) was cultured on MEAs, and...

journal_title：BioTechniques

authors： Rothermel A,Nieber M,Müller J,Wolf P,Schmidt M,Robitzki AA

更新日期：2006-10-01 00:00:00

abstract：:SNPCEQer identifies and reports SNPs in sequences obtained from the Beckman CEQ2000 DNA Analysis System. SNPCEQer aligns sequences obtained using CEQ2000 heterozygote detection analysis and reports discrepancies between individual sequences and the consensus sequence it generates from this set as SNPs when the individ...

journal_title：BioTechniques

authors： Flood EM,Tang F,Horvath MM,Pertsemlidis A,Garner HR

更新日期：2002-10-01 00:00:00

abstract：:A simple spectrophotometric method for measuring DNA in proliferating cells is described. The method is an adaptation of the widely used diphenylamine (DPA) reaction to examine DNA in cells grown in a 96-well plate. This assay was capable of detecting as little as 10 ng DNA and could be used to measure DNA in stored a...

journal_title：BioTechniques

authors： Natarajan N,Shambaugh GE 3rd,Elseth KM,Haines GK,Radosevich JA

更新日期：1994-07-01 00:00:00

abstract：:To increase the reproducibility and to reduce the false positives in the initial mRNA differential display, modified long composite primers were developed based on both mRNA differential display and RNA arbitrarily primed PCR fingerprinting methods. Ten-base nucleotides were added at the 5' ends of the primers used in...

journal_title：BioTechniques

authors： Zhao S,Ooi SL,Pardee AB

更新日期：1995-05-01 00:00:00

abstract：:Cytokines are pivotal to a balanced innate or cell-mediated immune response, can be indicative of disease progression and/or resolution, and are being evaluated as therapeutics. There is a need to purify and/or to measure key cytokines rapidly with accuracy, precision, and sensitivity. The current assay technologies, ...

journal_title：BioTechniques

authors： Bai H,Buller RM,Chen N,Boyle MD

更新日期：2002-01-01 00:00:00

abstract：:Quantitative real-time PCR has become a popular method to analyze and quantify changes in the copy number of mitochondrial DNA (mtDNA), and nuclear DNA (nDNA) is often used as an endogenous reference for mtDNA abundance. In our experience, using nDNA as a reference is problematic, due to differences in the extraction ...

journal_title：BioTechniques

authors： Myers MB,Mittelstaedt RA,Heflich RH

更新日期：2009-10-01 00:00:00

abstract：:The conventional method for cloning a DNA fragment is to insert it into a vector and ligate it. Although this method is commonly used, it is labor intensive because the ratio and concentrations of the DNA insert and the vector need optimizing. Even then, the resultant library is often plagued with unwanted plasmids th...

journal_title：BioTechniques

authors： Miyazaki K,Takenouchi M

更新日期：2002-11-01 00:00:00

abstract：:A technique that can be used to isolate vector/insert junctions from clones in vectors, such as yeast artificial chromosomes and P1s, and to sequence plasmid inserts more rapidly has been developed. A vector primer is combined with single, randomly chosen oligonucleotides in PCRs, to create pools of products. With 12-...

journal_title：BioTechniques

authors： Swensen J

更新日期：1996-03-01 00:00:00