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Thermo Scientific Gene Modulation DICTIONARY “AA” leader sequence: Historic nomenclature for siRNA design guidelines, specifying overhangs to be dTdT or UU. Not part of the siRNA molecule. 2’-ACE® chemistry: RNA synthesis chemistry proprietary to Thermo Scientific Dharmacon. The 2’ position of the nucleotide is protected with an acid labile ACE (2’ acetoxyethoxy) group. Acrylamide gel electrophoresis: Technique using a polymer gel for the high resolution separation of small fragments of DNA (10s to 100s of bases). Adenine: One of the four base groups present in either DNA or RNA. Abbreviated as “A”. Adherent cells: Cells that grow as a monolayer attached to the surface of the culture plate or flask. Agarose gel electrophoresis: Technique using a polysaccharide gel for the separation of DNA fragments up to 1Mb in length. alamarBlue®: A fluorometric assay used for measuring cell viability. (Available from BioSource Int’l). Allele: In diploid cells there are two copies of complementary DNA; when examining a specific nucleotide position or locus on the DNA each copy has an allele which can be the same as each other (homozygote) or different (heterozygote). Allelic discrimination: Multiplexed end point PCR assay that detects variants of a single DNA sequence (single nucleotide polymorphism) within a population. Individuals are classified as homozygous (only one type allele present) or heterozygous (one copy of each allele present). Amidite: Synthetic chemical building block for RNA or DNA synthesis. The natural building block is a nucleotide. Antisense strand: As part of an siRNA (or processed shRNA), it represents the strand that is complementary to the target mRNA; sometimes called the catalytic, targeting, or guide strand. ATG or AUG: Codon for methionine, the translation initiation codon or start codon. Barcode: A unique 60 nucleotide sequence contained within a shRNAmir construct that can be used to detect a specific construct from a mixed population. Enables pooled screening with viral RNAi. Not present in shRNA or SMARTvector constructs. Base: Component of nucleotides that determine the DNA and RNA alphabet: dA, dC, dG, dT in DNA, and A, C, G, U in RNA. Base pair (bp): Unit of length for double-stranded RNA or DNA. It is sometimes incorrectly used for unit of length for single-stranded DNA or RNA. bDNA: Branched DNA is a technique used for quantifying mRNA level. The bDNA Kit is called QuantiGene® Reagent System and is available from Panomics, Inc. Biomarker: A characteristic that is objectively measured as an indicator of normal cell and pathogenic processes or pharmalogical responses e.g. cell death, tumorigenesis or chemosensitisation. Biosafety Level 2: See ‘ BSL-2’ for definition. BLAST: Basic Local Alignment Search Tool. An algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA or RNA sequences. Branched DNA: See ‘bDNA’ for definition. BSL-2: Biosafety Level 2. A defined set of standards, practices, equipment and facilities associated with handling potentially infectious agents. Applies to most cell culture hoods. Catalytic strand: Same as the antisense, targeting, or guide strand in siRNA/miRNA. cDNA: Complementary DNA. DNA synthesized from a mature mRNA template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to clone eukaryotic genes in prokaryotes. Cell Confluency: Density of cells in a culture plate, expressed as %. Central polypurine tract: See ‘cPPT’ for definition. Clone: An exact copy of all or part of a macromolecule e.g. DNA. CMV: A type of promoter from Cytomegalovirus. This is a pol II (“2”) promoter often used to transcribe long constructs such as naturally ocurring mRNA or the vector cassette in the case of shRNA/ shRNAmir constructs. Coding sequence: Section of a gene or mRNA which codes for a protein. Codon: In mRNA, a codon is a sequence of three nucleotides which codes for the incorporation of a specific amino acid into the protein being produced. Complementary: Term used with nucleotides, sequence, or strand. Complementary pairs of nucleotides are G and C, A and U (in RNA), and A and T (in DNA). Complementary DNA: See ‘cDNA’ for defintion. Consensus sequence: A derived sequence inferred from the alignment and comparison of multiple imperfect sequences. Control: A reagent or experimental sample intended to confirm the specificity of results obtained with a test reagent. Cosuppression: Refers to the specific case of gene silencing in which RNA from a transgene and a homologous endogenous gene are suppressed at the same time. cPPT: Central polypurine tract. Helps translocation of a vector into the nucleus of non-dividing cells. Cytosine: One of the four base groups present in either DNA or RNA. Abbreviated as “C”. Deoxyribonucleic acid: See ‘DNA’ for definition. DICER: An enzyme complex which is active in the cytoplasm and is involved in processing long dsRNA and pre-miRNA into small interfering RNA and miRNA. DNA: Deoxyribonucleic acid. Polymers of nucleotides dA, dC, dG and dT. DNase: Deoxyribonuclease, a class of endonuclease enzymes which digest DNA. DNase I is the most common enzyme and digests single and double-stranded DNA. DOX: Doxycycline. A derivative of tetracycline, that is often used to turn on inducible promoters in shRNA/shRNAmir constructs. Doxycycline: See ‘DOX’ for definition. Drosha: An enzyme complex involved in processing precursor shRNA and primary miRNA into hairpin structures. This process occurs in the nucleus and is followed by DICER processing in the cytoplasm. dsRNA: Double-stranded RNA. Electroporation: A physical method to deliver oligonucleotides into hard-to-transfect or suspension cells using an electric current. Endogenous: Naturally present in the cell, e.g. endogenous gene, mRNA, protein, miRNA. Endonuclease: An enzyme which digests nucleic acids in the middle of the sequence e.g. restriction enzymes, DNase I, RNase A. EST: Expressed Sequence Tag. Partial sequence (500 -800 bp) of a cDNA with limited supporting information available, typically only a 3’ or 5’ end sequence. Produced by one-shot sequencing of a cloned mRNA. Exogenous: Artificially introduced into a cell, e.g. exogenous gene, mRNA, protein, miRNA. Exon: Segments of genomic DNA which will be incorporated into the final mature mRNA. Exons may include coding sequence, 5’ untranslated region or the 3’ untranslated region. Exonuclease: Enzyme which digests nucleic acids starting at one end. Expressed Sequence Tag: See ‘EST’ for definition. Expression ready: The cDNA or ORF is already cloned into the expression vector for immediate use in mammalian cells. Extinction Coefficient, ε, (L/mol•cm): The most quantitative measure for RNA is Beer’s Law: Absorbance (260 nm) = (ε)(concentration) (path length in cm), where ε is the molar extinction coefficient (provided on the siRNA Product Transfer Form supplied with the order). FACS: Fluorescent Activated Cell Sorting. A means of measuring certain physical and biochemical characteristics of cells or particles as they travel in suspension one by one past a sensing point. Fluorescence: Light emitted after absorption of light at a lower wavelength. Fluorescent Activated Cell Sorting: See ‘FACS’ for definition. Fluorophore / Fluorochrome: A small molecule or part of a larger molecule that can fluoresce. Gag: A lentiviral packaging element that encodes for a structural precursor protein. Gateway adapted: A cloning system that enables efficient transfer of DNA-fragments between plasmids using a proprietary set of recombination sequences. It has effectively replaced the use of restriction endonucleases and ligases. This process is patented by Life Technologies (formerly Invitrogen). GC Content: Specific for an RNA or DNA sequence. The number of nucleotides G and C in a sequence, expressed as percent of total nucleotides. For siRNAs, only one strand needs to be used for calculating. Gel: Short for PAGE (PolyAcrylamide Gel Electrophoresis). A method for assessing size, integrity, and purity of DNA, RNA and protein. Gene: A DNA sequence that encodes a specific protein. This is a permanent copy within the cell and (generally) is not susceptible to degradation. Gene Ontology: A method of organizing gene products based on three general principles: molecular function, biological process and cellular component. These classifications can be used to generate lists of related gene products, such as kinases (molecular function), genes involved in apoptosis (biological process), or genes present in the cell membrane (cellular component). Genetic marker: Known location on a chromosome that can be used to identify the region of the DNA by phenotype or polymorphism. Genome: Total DNA contained within each cell of an organism, e.g. the human genome contains 6 x 109 base pairs of DNA per cell. Genotype: Set of alleles that determines the expression of a particular characteristic or trait (phenotype). Guanine: One of the four base groups present in either DNA or RNA. Abbreviated as “G”. Glycerol Stock: Frozen stock cultures of bacteria or yeast provided in liquid media. Guide strand: Same as the antisense, catalytic, or targeting strand in siRNA/miRNA. Heat map: A format for displaying microarray analysis data. Typically green lines indicate decreases in mRNA levels and red lines indicate increases in mRNA levels. Helicase: An enzyme function associated with RISC that unwinds the siRNA into two strands to allow loading of one single strand into the catalytic site. Hexadimethrine bromide: See ‘Polybrene’ for definition. High Performance Liquid Chromatography: See ‘HPLC’ for definition. High-titer viral particles: Transduction-ready high-titer lentiviral particle format removes the need to prepare plasmid DNA, package and then purify each lentivirus preparation before use. High titer is typically ~ 1 x 10 TU/mL. TU refers to transduction unit/individual viral particle. Housekeeping gene: A gene that is expressed in all cell types and at a constant level during all stages of the cell cycle. Generally used as a control gene. Recent studies suggest even housekeeping genes can vary in their expression levels, therefore several housekeeping genes are often used to normalize data, especially in PCR. HPLC: High Performance Liquid Chromatography. A method for assessing integrity, and purity of DNA, RNA and protein (and other molecules). Hybridization: The reaction by which complementary strands of nucleic acid pair and bind together. Imperfect hybrids can also form but these are much less stable than perfectly matching sequences. Immortalized cell line: A cell line that has acquired the ability to proliferate indefinately through either random mutation or deliberate modification. In contrast to primary cells which are cultured directly from the subject. In vitro: Describes biological experiments performed outside of a whole animal (see in vivo), such as in cultured cells. In vivo:Describes biological experiments performed in live, whole laboratory animals. Insert: The target sequence being cloned within a plasmid clone, rather than the host vector sequence. Intercalating dye: Non-specific fluorescent dye which fluoresces when bound within the minor groove of double-stranded DNA e.g. SYBR Green. Interferon response: A cellular immune response which can ultimately lead to cell death. This reponse can be triggered by long dsRNA (~> 30 nucleotides) or even high concentrations of siRNAs. Internal Ribosomal Entry Site: See ‘IRES’ for definition. IRES: Internal Ribosomal Entry Site. A sequence that allows translation inititation in the middle of a mRNA sequence, rather than only at the 5’ end. Isoforms: Used in “protein isoforms”, which are versions of a protein with some small differences in their amino acid sequences. Encoded by mRNA variants. kb: Abbreviation for kilobase, one thousand bases. Knockdown: Reduction in a target mRNA or protein level as a result of RNAi. Expressed as percent of control. Synonym: Silencing. Knock-out: Technique for deleting, mutating or otherwise inactivating a gene within an organism. Lentivirus: A genus of the Retrovirus family. Lentiviruses can deliver a significant amount of genetic information into the DNA of the host cell, so are one of the most efficient gene delivery vectors. This class of virus is able to transduce non-dividing, primary cells. Library: A molecular biology term that refers to a collection of molecules that is screened to find the desired one. For example, an siRNA library is a collection of siRNAs that target different genes, and is screened to identify which gene affects the biological process of interest. Ligase: Enzyme which can join pieces of DNA with compatible ends together, e.g. T4 DNA ligase. Ligation: The process of splicing two pieces of DNA together. Lipid: Jargon for transfection reagents that are composed of cationic (positively-charged) lipids. Also called a liposome. LNA: Locked Nucleic Acid. Often referred to as inaccessible RNA, LNA’s are a modified RNA nucleotide used to increase the sensitivity and specificity of an RNA sequence. Often used in microarrays, antisense experiments, as well as by some siRNA and miRNA inhibitor vendors. Locked Nucleic Acid: See ‘LNA’ for definition. Locus (pl. Loci): The location of a gene on a chromosome. Long terminal repeat: See ‘LTR’ for definition. LTR: Long terminal repeat. Homologous regions, consisting of 600-900 nucleotides, in the lentiviral vector that are required for replication, integration, and expression of viral RNA. MALDI-TOF: Matrix-Assisted Laser Desorption/Ionization-Time Of Flight mass spectrometry. Method for assessing integrity and molecular weight of DNA, RNA and protein (and other molecules). Mass spec: Mass spectrometry. A method for assessing size and integrity of DNA, RNA and protein (and other molecules). Medium/Media (pl.): As in “cell culture medium”; a solution used to grow cells in and contains nutrients necessary for their growth. microRNA: See ‘miRNA’ for definition. Minor groove binder (MGB): Naturally occurring antibiotic molecule that adopts a crescent shape which fits into the minor groove of DNA. Integration of a MGB into a DNA hybridization probe increases the Tm of the probe and reduces the length of the required probe. MIQE: Minimum Information for publication of Quantitative realtime PCR Experiments. Microarray: A multiplex technology consisting of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, known as probes (or reporters). This can be a short section of a gene or other DNA element that are used to hybridize a cDNA or miRNA under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore. miRBase: A central repository for miRNA nomenclature, sequence data annotation and target prediction. miRNA: Abbreviation for microRNA. Short endogenously expressed RNA molecules that function as gene expression modulators. miRNA scaffold: A native non-coding RNA into which sequences targeting the gene of interest are cloned. This scaffold is readily processed by the endogenous RNAi machinery, providing enhancedperformance over other expression cassettes. Mismatch: Non-complementary nucleotide pairs (in the context of matching base pairs). Mods (Modifications): Chemical modifications to the standard A, C, G, U nucleotides. MOI: Multiplicity of infection: the ratio of vector transducing particles to cells. Molecular Weight (g/mol): Sum of atomic weights of all atoms in a molecule. mRNA: Messenger RNA molecule. Transcription product of a gene that gets translated into a protein. Also called message or transcript. Multiplicity of infection: See ‘MOI’ for definition. NCBI: National Center for Biotechnology Information (http://www. ncbi.nlm.nih.gov/). Public databases containing information on DNA, RNA, and protein sequences, function, and publications. nM (nanomolar): A concentration unit that is defined as nanomole per liter. Non-catalytic strand: Same as the sense, passenger, or nontargeting strand in siRNA/miRNA. Northern Blot: A method for detecting specific mRNAs using radioor chemiluminescent-labeled DNA probes. Nuclease: Enzyme that degrades nucleic acids; specific enzymes can be DNA or RNA specific, act on single or double-stranded sequences or be non-specific. Nucleofection: A transfection method which enables transfer of nucleic acids such as DNA, RNA or siRNA into cells. Specifically relates to transfection via the physical method of electroporation with the Amaxa Nucleofector system. Nucleotide (nt): Molecules that consist of a base, a sugar and one or more phosphates. Naturally present with one of four bases to make A, C, G, U or T. Also used as unit of length for single-stranded DNA or RNA. Off-target: A gene other than the intended target that is also regulated by the siRNA. When data for multiple genes are displayed (e.g. from a microarray), it is called the off-target signature of the siRNA. Oligonucleotide: Polymer of nucleotides (nt), generally less than 100 nt. Also called an oligo. Open Reading Frame: See ‘ORF’ for definition. ORF: Open Reading Frame. The portion of an mRNA that contains a sequence of bases that could potentially encode a protein. The 5’ untranslated region and 3’ untranslated region are on either side of this section. Overhang: Two nucleotides on the 3’-end of an siRNA strand that do not have complementary nucleotides in the complementary strand. Packaging: Creation of viral particles that can be used to deliver and express a specific gene targeting sequence (as an shRNA) into mammalian cells. Packaging plasmid: Lentiviral vectors that contain all necessary elements to efficiently generate active viral particles. PAGE: Polyacrylamide Gel Electrophoresis. A method for assessing size, integrity, and purity of DNA, RNA and protein. Sometimes described as denaturing (to assess size of a single-stranded DNA or RNA) or non-denaturing (to assess duplexing of two DNA or RNA strands). Passenger strand: Same as the sense or non-catalytic strand in siRNA/miRNA. PCR: Polymerase Chain Reaction. A method for amplifying specific DNA or RNA. For RNA, a reverse transcription step before PCR is necessary; this is termed RT-PCR. When performed as quantitative assay, also termed quantitative PCR (qPCR) or real-time PCR. Phenotype: Observable features of cells or organisms, e.g. shape, size, differentiation state. Plasmid: Additional piece of circular DNA present in bacteria into which target DNA can be inserted to be replicated by the host bacteria, e.g. pBR322 and pUC18. Pol: A lentiviral packaging element that encodes for a structural precursor protein. Polyacrylamide Gel Electrophoresis: See ‘PAGE’ for definition. Post-transcriptional regulation: Processes occurring after transcribing the mRNA which affects the amount of protein produced from a gene. Includes RNA processing efficiency and RNA stability. Polybrene: Hexadimethrine bromide. Has been shown to enhance transduction of mammalian cells by 2-10 fold by binding to the cell surface and neutralizing surface charge. Polymerase Chain Reaction: See ‘PCR’ for definition. Polymerase: Enzyme which uses an existing strand of template to make a complementary copy by linking individual nucleotides together, e.g. DNA polymerase used in PCR. Polymorphism: DNA sequence variations at a specific position or locus which results in variation within a population. Some diseases are a direct result of polymorphisms. Preliminary miRNA: See ‘pre-miRNA’ for definition. Pre-miRNA: Preliminary miRNA. miRNAs are transcribed as primiRNAs, which are processed in the nucleus by Drosha and Pasha to hairpin structures of about ~70 nucleotide called pre-miRNAs. These precursors are exported to the cytoplasm by exportin5, where they are subsequently processed by the enzyme Dicer to a ~22 nucleotide mature miRNA. Primary cells: Cells that are harvested from whole animals and grown in culture. They generally survive for only a limited time, unlike immortalized cell lines that can divide infinitely. Primary miRNA: See ‘Pri-miRNA’ for definition. Primer: Or oligonucleotide. Short piece of nucleic acid sequence (6 to 50 bases) used to prime DNA synthesis. Pri-miRNA: Primary miRNA. miRNAs are transcribed as pri-miRNAs, which are processed in the nucleus by Drosha and Pasha to hairpin structures of about ~70 nucleotide called pre-miRNAs. These precursors are exported to the cytoplasm by exportin5, where they are subsequently processed by the enzyme Dicer to a ~22 nucleotide mature miRNA. Probe: Fragment of DNA or RNA that is labeled with a radiolabel or fluorescent tag which when hybridized to the sequence of interest allows detection and quantitation. Promoter: A region of DNA that facilitates the transcription of a particular gene. Promoters are typically located near the genes they regulate, on the same strand and upstream (towards the 5’ region of the sense strand). Pulse field gel electrophoresis: Technique to size separate very large fragments of DNA; the voltage is applied alternatively along both axes (length and width) forcing even large molecules to separate. qPCR: Quantitative PCR. Based on standard PCR, qPCR enables both detection and quantification of one or more specific sequences in a DNA sample. Quantitative PCR: See ‘qPCR’ for definition. RefSeq: Curated database at NCBI (see entry for NCBI for details). This is the mRNA sequence database used by Thermo Scientific Dharmacon for siRNA designs and Thermo Scientific Open Biosystems shRNA designs. Replication incompetent: Lentiviral particles that are incapable of producing additional viral particles, due to the elimination of wildtype enhancers in the long terminal repeat region. Restriction enzyme: Class of enzymes, generally from bacteria which are able to recognize and cut specific sequences in DNA e.g. ECORI. Retrovirus: An RNA virus that is replicated in a host cell via the enzyme reverse transcriptase to produce DNA from its RNA genome. This class of virus is able to transduce dividing cells only. Reverse transcriptase: DNA dependant RNA polymerase originally isolated from retroviruses which produces a copy of DNA (complementary DNA) from an RNA temperate. Reverse Transfection Format: See ‘RTF’ for definition. Ribonuclease: See ‘RNase’ for definition. Ribonucleic acid: See ‘RNA’ for definition. RISC: RNA Induced Silencing Complex. Complex of multiple proteins and siRNA, part of the RNAi pathway. RNA: Ribonucleic acid. Long polymers of ribonucleotides A, C, G and U that naturally occurs in cells. This can be coding RNA, termed mRNA, which is translated into protein. Other types of RNA includerRNA, tRNA, etc. These have other functions within cells and do not lead to proteins. RNA Induced Silencing Complex: See ‘RISC’ for definition. RNAi: See ‘RNA interference’ for definition. RNA interference (RNAi): A cellular mechanism by which the expression of a target gene is reduced due to the presence of siRNA or miRNA. RNAi Rescue experiment: Following knockdown of a gene by an siRNA or shRNA, application of the relevant ORF should recover expression of the gene. If expression is not retrieved, the phenotype was most likely due to an off-target effect. RNase: Ribonuclease. An enzyme responsible for cleaving and degrading RNA. When associated with RISC it leads to cleavage of the target mRNA. When part of experimental contamination (bench, hands, buffers, etc) it can lead to degradation of RNA. RTF: Reverse Transfection Format, which involves introduction of siRNA + transfection reagent to cells while the cells are still in a suspension state prior to adhering to the plate or flask. S1 nuclease: Enzyme that digests only single-stranded nucleic acids. Screen: A process for quickly identifying which molecule in an experimental pathway, process, etc is of interest, using a library of molecules such as siRNA/miRNA. Seed region: Nucleotide positions 2 through 7/8 of an miRNA or the antisense strand of an siRNA. Often called the hexamer, heptamer, or recognition region. Self Inactivating: See ‘SIN’ for definition. Sense strand: When part of an siRNA, it is identical to the target mRNA region; sometimes called the passenger or non-catalytic strand. Sequence: The arrangement of nucleotides in a DNA or RNA molecule, or amino acids in a protein. Short hairpin RNA molecule: See ‘shRNA’ for definition. Short tandem repeat (STR): Pattern of two or more nucleotides in DNA, repeated directly adjacent to each other. Polymorphisms occur when the number of repeats differs between individuals; these variances are used in the forensic analysis to create genetic profiles of individuals. shRNA: Short hairpin RNA molecule. Typically used by investigators trying to develop a stable cell line. The shRNA is cleaved into an siRNA by Dicer. shRNAmir: An shRNA construct based on a naturally occurring primicroRNA sequence in which the sequence for the mature miRNA is removed from the hairpin and replaced with the silencing sequence of interest. SIN: Self Inactivating. Self-inactivating lentiviral and retroviral vectors are constructed by deleting the transcriptional enhancers or the enhancers and promoter in the U3 region of the 3’ UTR. After one round of vector replication, these changes are copied into both the 5’ and the 3’ LTRs producing an inactive provirus that is replication-incompetent. Single Nucleotide Polymorphism: See ‘SNP’ for definition. siRNA: Small interfering RNA. Double-stranded RNA, 19 nucleotide core sequence, 2 nucleotide overhang on the 3’ end of each strand. Small interfering RNA: See ‘siRNA’ for definition. SNP (pronounced “snip”): Single Nucleotide Polymorphism. DNA sequence variation (mutation) occurring when a single nucleotide - A, T, C, or G - in the genome differs between members within a species. SNPs may result in a disease. Southern blot: Method for detecting specific DNA sequences using radio or chemiluminescent DNA probes. Splice variant: Result of alternative processing or splicing of premRNA in eukaryotes by differential inclusion, skipping or exclusion of exons (and introns) which allows a single gene to code for multiple proteins. ssRNA: Single-stranded RNA. Sticky ends: After digestion of DNA with certain restriction enzymes the ends left have one strand overhanging the other to form a short (4 bases) single-stranded segment which can easily anneal to other complementary ends. Stringency: The conditions of hybridization; when varied the salt concentration and temperature may allow the probe to only hybridize to it’s exact complement (high stringency) or related sequences (low stringency). Increasing temperature or reducing the salt concentration increases stringency. Stop codon: Also known as a termination codon. A nucleotide triplet within messenger RNA that signals the termination point for translation. Suspension cells: Cells that grow without attaching to a surface (see adherent cells). Taq polymerase: DNA polymerase from Thermophilus aquaticus; enzyme is very stable at high temperatures and is able to maintain activity during the repeated raised temperatures of PCR. TAT: A lentiviral packaging element required for the efficient elongation of nascent viral transcripts. Required for packaging GIPZ, TRIPZ and pLOC. Tetracycline Response Element: See ‘TRE’ for definition. Thymine: One of the four base groups present in DNA. Abbreviated as “T”. Tm: Melting temperature of an oligonucleotide. A property of G/C content and thus a measure of stability of two annealed strands. Transcription: The process of copying DNA to RNA by an enzyme called RNA polymerase. When done artificially outside of a whole cell, it is called in vitro transcription (IVT). Transcription factor: Protein involved in the transcription of genes; can be tissue-specific or generic. Transducing Unit: See ‘TU’ for definition. Transduction: The transfer of viral, bacterial, or both bacterial and viral DNA from one cell to another using a viral vector. Transduction Efficiency: Refers to the fraction of cells that successfully integrate one or more viral genomes during the transduction process. Transfection: A method for delivering DNA or RNA into mammalian cells using a complexing reagent such as cationic lipids. Transgenic: Organism that carries experimentally introduced DNA; involves the injection of DNA into a fertilized embryo at the pronuclear stage which is then incorporated into the genome of the embryo. Translation: The process of making protein from an mRNA. When done artificially outside of a whole cell, it is called in vitro translation. TRE: Tetracycline Response Element. Often used in inducible vectors. TU: Transducing Unit. Unit of measure that refers to the number of viral particles which can transduce a population of cells and integrate into the host genome. Untranslated Region: See ‘UTR’ for definition. Uridine: One of the four base groups present in RNA. Abbreviated as “U”. UTR: Untranslated Region. A portion of an mRNA that contains important biological signals for gene regulation, present on each side of the open reading frame. Variants: As in “mRNA variants”, which are versions of an mRNA with differences in their nucleotide sequences and may code for different protein isoforms. Vector: A vehicle for delivering and expressing an exogenous DNA sequence in a cell; usually a plasmid or virus. Vesicular Stomatitis Virus glycoprotein: See ‘VSVg’ for definition. Viability: As in “cell viability”. A measure of cell health expressed as percent of control. Viral Particle: Intact virus capable of transducing cells and expressing a sequence of interest that target specific genes for knockdown via the RNAi pathway. Viral titer: The number of transducing units present in a given volume (1 mL). Titer can be assessed by a number of methodologies including antibody and PCR-based methodologies, FACS analysis and colony formation. VSVg: Vesicular Stomatitis Virus glycoprotein. An envelope protein derived from vesicular stomatitis virus. VSVg has been shown to provide broad tropism so when incorporated into lentiviral constructs, it enables transduction of a broad range of cell types. Western Blot: A method for detecting a specific protein in cell lysates. An antibody is used as a probe to detect the protein of interest. Woodchuck Hepatitis Virus Post-Transciptional Regulatory Element: See ‘WPRE’ for definition. WPRE: Woodchuck Hepatitis Virus Post-Transciptional Regulatory Element. Increases transgene expression from a variety of viral vectors. Thermo Scientific Gene Modulation DICTIONARY www.thermoscientific.com/gen US Literature # 0007506D02U © 2010 Thermo Fisher Scientific Inc. All rights reserved. QuantiGene is a trademark of Bayer. alamarBlue is a trademark of Accumed International, Inc. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.