serial analysis of gene expression sage practical approach

... Jong and Nicole Datson Table Characteristics of differential display and serial analysis of gene expression Differential display Serial analysis of gene expression Requirements Standard molecular ... amounts of starting material and making the monitoring of expression of thousands of genes simultaneously possible Second, the increasing knowledge of DNA sequences of a large number of genes and ... tens of thousands of genes each expressed at a different level, characterization of gene expression profiles is not a straightforward task The set of genes expressed and the stochiometry of the...

Ngày tải lên: 11/04/2014, 09:51

... 2008, 5:77 Figure Sensitivity of the one-step RT-PCR assay Sensitivity of the one-step RT-PCR assay Example of amplification results of ten-fold serial dilutions of in-vitro transcribed RNA H10N7 ... of NA gene fluids One-stepusing animal samples from allantoic from all NA One-step RT-PCR amplification of NA gene from all NA subtypes using animal samples from allantoic fluids A fragment of ... of 1,101 fulllength NA sequences of the subtypes, of a range of host species and from different geographical locations were retrieved and aligned using Biological Sequence Alignment editor software...

Ngày tải lên: 20/06/2014, 01:20

... in the amplification of the original coaD gene The use of the Nco I restriction site dictates what the first nucleotide of the next triplet codon must be (G) In the coaD gene, however, the second ... protein will be glutamate instead of glutamine) An alternative strategy which will result in the amplification of the original gene is described in Utilisation of the Nco I site 3'-end primer No ... (CG) BamH I restriction site (GGATCC) Complement of stop codon (CTA) Overlap with the strand complement to the 3'-end of the coaD gene Estimated Tm of 60°C [8 * (A+T) + 11 * (C+G)] GC content is...

Ngày tải lên: 14/07/2015, 23:53

... either 100 pg of DENV-1-, ng of DENV-2-, 100 pg of DENV3- or ng of DENV-4-infected C6 ⁄ 36 cells total RNA was used for cocktail PCR The primer cocktail was composed of 100 nm each of 1G1P1, 1G3P6, ... Putnak R, Mammen MP, Li T & Zhang C (2008) Molecular genotyping of dengue viruses by phylogenetic analysis of the sequences of individual genes J Virol Meth 154, 175–181 31 Schreiber MJ, Holmes EC, ... Effect of geographical variation in dengue virus on the performance of the primer cocktail Each of the four serotypes of dengue virus can be classified into several genotypes, defined as a group of...

Ngày tải lên: 14/02/2014, 19:20

... (1999) Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags Nucleic Acids Res 27, e17 Chen JJ, Rowley JD & Wang SM (2000) Generation of longer cDNA fragments from serial analysis ... analysis of gene expression tags for gene identification Proc Natl Acad Sci USA 97, 349–353 Richards M, Tan SP, Chan WK & Bongso A (2006) Reverse serial analysis of gene expression (SAGE) characterization ... (RAST-PCR) [15], generation of longer cDNA fragments from SAGE tags for gene identification (GLGI) [16] and reverse SAGE (rSAGE) [17]] hardly generate the 3¢-fragment sequences of these unmatched...

Ngày tải lên: 07/03/2014, 04:20

... Many studies of genetic relatedness leading to the construction of phylogenetic trees are based on sequence analysis of the 16S region An extensive diagnostic system based on 16S rRNA gene amplification ... enzyme analysis Sachse Fig Structural organization of ribosomal RNA genes in bacteria Due to its manageable size of approx 1500 bp, the 16S rRNA gene has become the best characterized part of the ... yield (expressed as quotient of the number of molecules of PCR product and the initial number of target molecules), n is the number of cycles, and ε is the mean efficiency of all cycles with ≤ ε ≤...

Ngày tải lên: 11/04/2014, 10:01

... appropriate control genes, as any variation in the expression of the reference gene between sample groups will reduce the sensitivity of the assay to detect changes in the expression of genes of interest ... deviations of reference gene expression as determined by GeNorm are shown Abbreviations: Sumv: Sum of viral infection GeNorm values; sumRGC: sum of reference gene GeNorm values Table 3: Reliability of ... investigating the effects of viruses on host cell gene expression as viruses can interfere with host cell pathways, the components of which traditional housekeeping genes often encode These include...

Ngày tải lên: 18/06/2014, 18:20

... Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region J Gen Virol 1993, 74 ( Pt 11):2391-2399 Martell M, Esteban JI, Quer J, Genesca ... amplification of a portion of the sequences in the target population and is a result of varying primer affinities for the heterogeneous template molecules during PCR Primer bias is unavoidable in HCV genetic ... region [7,8] Analysis of the NS5B region encoding the viral RNA polymerase from a wide range of HCV isolates led to the classification of HCV into six major genotypes and a series of subtypes...

Ngày tải lên: 19/06/2014, 08:20

... appropriate control genes, as any variation in the expression of the reference gene between sample groups will reduce the sensitivity of the assay to detect changes in the expression of genes of interest ... deviations of reference gene expression as determined by GeNorm are shown Abbreviations: Sumv: Sum of viral infection GeNorm values; sumRGC: sum of reference gene GeNorm values Table 3: Reliability of ... investigating the effects of viruses on host cell gene expression as viruses can interfere with host cell pathways, the components of which traditional housekeeping genes often encode These include...

Ngày tải lên: 20/06/2014, 01:20

... Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region J Gen Virol 1993, 74 ( Pt 11):2391-2399 Martell M, Esteban JI, Quer J, Genesca ... amplification of a portion of the sequences in the target population and is a result of varying primer affinities for the heterogeneous template molecules during PCR Primer bias is unavoidable in HCV genetic ... region [7,8] Analysis of the NS5B region encoding the viral RNA polymerase from a wide range of HCV isolates led to the classification of HCV into six major genotypes and a series of subtypes...

Ngày tải lên: 20/06/2014, 04:20

... effects, including suppression of the HPA axis marker corticosterone, induction of the gluconeogenesis gene tyrosine aminotransferase (TAT), and effects on markers of bone homeostasis These data ... day of the study Two injections of 100 μl of collagen/adjuvant were made, one into the base of the tail and the other further up the back, separated by approximately 1.5 cm A boost injection of ... alter expression of various markers of osteoporosis, including osteocalcin and structural measures of bone density and quality Female mice were treated orally twice daily with various doses of pred-...

Ngày tải lên: 09/08/2014, 01:22

... Models were delineated from micrographs of the Hartig net and from possible alternatives in growth of hyphae (Fig 3) Area, perimeter and length of hyphal walls of the models were measured with Mop-Videoplan, ... system (Zeiss-Kontron), using standard software The surface/volume ratios of the different systems were calculated on the basis of an average pm diameter of hyhae Results frequently be found separated ... Measurements from these models of area and perimeter of hyphal complex and length of hyphal walls are presented in Table I (Trinci, 1984; Prosser, 1983) The result is pinnate growth of scattered hyphae,...

Ngày tải lên: 09/08/2014, 04:20

... ME, Su IJ: Upregulation of tumor necrosis factor-alpha gene by Epstein–Barr virus and activation of macrophages in Epstein–Barr virus-infected T cells in the pathogenesis of hemophagocytic syndrome ... epithelial and endothelial cells Salivary glands are a major site of production of HHV7 [9,52] HHV6 and HHV7 antigenemia occurs in the setting of CMV reactivation in transplant patients [53] with the ... selection of latently infected B cells J Immunol 2000, 165:2975-2981 20 Decker LL, Klaman LD, Thorley-Lawson DA: Detection of the latent form of Epstein–Barr virus DNA in the peripheral blood of healthy...

Ngày tải lên: 09/08/2014, 06:22

... the true amount of the protein in cells or tissues Quantitative analysis of mRNA as presented here has the unique advantage in providing quantitative information of the gene expression concerned ... general category of reduced expression of E-cadherin staining Competing interests In conclusion, using real time quantitative PCR we have shown that there is no difference in the expression of ... conflicting reports as to the usefulness of E-cadherin expression as an independent prognostic marker in invasive breast cancer [14-20] In general, retention of E-cadherin expression correlates with well-differentiated,...

Ngày tải lên: 09/08/2014, 07:21

... examination of amplicons > 50% GC suggested an effect of sequence context We found the %GC of a 250-bp window centered on the amplicons a better predictor of under-coverage than the %GC of the amplicons ... sequencing in cancer and medical genetics, the major sequencing applications in terms of bases generated Solving the loss of AT-rich loci remains a challenge, but has less of an impact on human genome ... sample with a range of base composition spanning almost the entire spectrum as a test substrate throughout our investigation of sources of bias We started with an equimolar mixture of DNA prepared...

Ngày tải lên: 09/08/2014, 22:23

... Evaluation of two set of primers for detection of immediate early gene UL123 of human cytomegalovirus (HCMV) Mol Biotechnol 2008, 38:65-70 Habbal W, Monem F, Gartner BC: Comparative evaluation of published ... Calculations of Ct, preparation of standard curve and quantification of each sample’s DNA were performed by the Option Monitor Software According to the manufacture’s instructions, the detection limit of ... (DaAn Gene Co., Ltd., Zhongshan University, China), as described by Sun Z et al [39] The kit contains reagents and enzymes for the specific amplification of a 86-bp region of the IE1 gene of HCMV...

Ngày tải lên: 12/08/2014, 04:20

... characterization of the poxvirus BeAn 58058 Arch Virol 1998, 143:1171-86 Hosamani M, Bhanuprakash V, Scagliarini A, Singh RK: Comparative sequence analysis of major envelope protein gene (B2L) of Indian ... based on computer simulation of different combinations of several published primer pairs, using software available online [19] Two exclusive and highly conserved genes were targeted by nested-multiplex ... expected fragments of 170 bp (OPV) and 592 pb (PPV)], described as follows In the first step, μL of template were added to 18 μL of the PCR reaction mixture containing 0.4 mM of OPV primers (VGF-F...

Ngày tải lên: 12/08/2014, 04:20

... change of the sample in a temperature range of 60°C to 90°C The derivative of the measured fluorescence plotted against temperature was displayed using the HR-1 software and the peak of these ... Author details Department of Laboratory Medicine, Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada 2Department of Pediatrics, University of Botswana, Gaborone, Botswana ... hour, prospective studies of this assay are warranted to evaluate the clinical impact of the assay on the management of patients with pharyngitis Slinger et al Annals of Clinical Microbiology...

Ngày tải lên: 12/08/2014, 17:20

... consisting of 101 and 103 copies of XMRV VP62 plasmid DNA diluted in a background of μg of human PBMC DNA, respectively Figure Absence of XMRV/MuLV sequences by real-time PCR in PBMC DNA of persons ... DNA H2O H2O amount of starting DNA Specifically, the assays of Lo et al and Lombardi et al can at best detect copy of XMRV/MuLV in a background of 30 to 50 ng and 100 to 250 ng of DNA respectively ... on the right of the WB Sizes of expected viral proteins are provided to the left of the WB c Representative WB results for CFS cases and persons without CFS Lane 1, 1:250 dilution of anti-Friend...

Ngày tải lên: 13/08/2014, 01:20

... 470-480 Lapta GE, Shakhbazov VG (1986) Analysis of specificity of ectopic conjugation of telomeric ends of Drosophila melanogaster polytene chromosomes Genetika (USSR) 22, 787-792 Renkawitz-Pohl ... of broken chromosomes These additions serve the role of telomeres in stabilizing the tips against the loss of DNA during replication Moreover, the addition of the He-T sequences to the ends of ... situ comparison of salivary gland chromosomes and metaphase chromosomes from other tissues, in order to allow an estimation of the number of copies of Dm665 that occur in the tips of metaphase chromosomes...

Ngày tải lên: 14/08/2014, 20:20