Evolutionary population genomics
... Phenotypic information from natural populations and laboratory crosses ...
... Phenotypic information from natural populations and laboratory crosses ...
Supplementary Methods S2: Exome Sequencing
... As muTector attempts to call mutations it also generates a coverage file in a wiggle file format(9), which indicates for every base whether it is sufficiently covered in the tumor and normal to be sensitive enough to call mutations. We currently use cutoffs of at least 14 reads in the tumor and at l ...
... As muTector attempts to call mutations it also generates a coverage file in a wiggle file format(9), which indicates for every base whether it is sufficiently covered in the tumor and normal to be sensitive enough to call mutations. We currently use cutoffs of at least 14 reads in the tumor and at l ...
Supplementary Information
... attP1-BglII and attP2-XhoI from pDONR-207 (Invitrogen) as a template, and then inserted into the BglII and XhoI sites located at the border of two parts of the divided Luc gene. The resultant plasmid was named pSSARL-GwBP. The nucleotide sequence of the pSSARL-GwBP is shown in Supplementary Figure. ...
... attP1-BglII and attP2-XhoI from pDONR-207 (Invitrogen) as a template, and then inserted into the BglII and XhoI sites located at the border of two parts of the divided Luc gene. The resultant plasmid was named pSSARL-GwBP. The nucleotide sequence of the pSSARL-GwBP is shown in Supplementary Figure. ...
Nucleic acid hybridisation and polymerase chain reaction
... After a genomic p o r t i o n is chosen, a search is c o n d u c t e d for pairs of 18-24 m e r oligonucleotides with several characteristics: - 40-60% G+C content - absence of polypurines or polypirimidines - absence of secondary structure - absence of complementarity, particularly at the 3 ' end, ...
... After a genomic p o r t i o n is chosen, a search is c o n d u c t e d for pairs of 18-24 m e r oligonucleotides with several characteristics: - 40-60% G+C content - absence of polypurines or polypirimidines - absence of secondary structure - absence of complementarity, particularly at the 3 ' end, ...
Chromosome Locations of the MYB Related Genes, AMYB and
... are readily distinguishable from mouse AMYB fragments (Fig. 2A, Lane 9). The two diagnostic human AMYB fragments are present in hybrid DNA in lanes 2-4, 6, and 7 (Fig. 2A) which contain region Seen—»8q24 in common; AMYB negative hybrids contain no chromosome 8 (Fig. 2A, Lane 5) or contain region ...
... are readily distinguishable from mouse AMYB fragments (Fig. 2A, Lane 9). The two diagnostic human AMYB fragments are present in hybrid DNA in lanes 2-4, 6, and 7 (Fig. 2A) which contain region Seen—»8q24 in common; AMYB negative hybrids contain no chromosome 8 (Fig. 2A, Lane 5) or contain region ...
Alisch RS, Wang T, Chopra P, Visootsak J, Conneely KN, Warren ST . Genome-wide analysis validates aberrant methylation in fragile X syndrome is specific to the FMR1 locus. BMC Med Genet. 2013 Jan 29;14:18. doi: 10.1186/1471-2350-14-18.
... analyzed each locus using a linear mixed-effects regression model that adjusted for age (see Methods) and identified 17 differentially methylated probes, 15 of which are annotated to the FMR1 promoter or gene body: 14 FXS-methylated loci and 1 FXS-demethylated locus (Bonferroni <0.05; Figure 1 A, B; ...
... analyzed each locus using a linear mixed-effects regression model that adjusted for age (see Methods) and identified 17 differentially methylated probes, 15 of which are annotated to the FMR1 promoter or gene body: 14 FXS-methylated loci and 1 FXS-demethylated locus (Bonferroni <0.05; Figure 1 A, B; ...
The application of molecular genetics to detection of
... level. There have been few definitive findings which hold up in more than a single model system, and any genetic or environmental factor that appears critical in one case can be excluded in another. The analysis of single gene mutations using RFLPs for linkage studies has had considerable success in ...
... level. There have been few definitive findings which hold up in more than a single model system, and any genetic or environmental factor that appears critical in one case can be excluded in another. The analysis of single gene mutations using RFLPs for linkage studies has had considerable success in ...
Document
... Bitter-tasting compounds are recognized by receptor proteins on the surface of taste cells. There are approximately 30 genes for different bitter taste receptors in mammals. The gene for the PTC taste receptor, TAS2R38, was identified in 2003. Polymerase Chain Reaction (PCR) is used to amplify a sho ...
... Bitter-tasting compounds are recognized by receptor proteins on the surface of taste cells. There are approximately 30 genes for different bitter taste receptors in mammals. The gene for the PTC taste receptor, TAS2R38, was identified in 2003. Polymerase Chain Reaction (PCR) is used to amplify a sho ...
Carolina: Using SNP`s to Predict Bitter
... Bitter-tasting compounds are recognized by receptor proteins on the surface of taste cells. There are approximately 30 genes for different bitter taste receptors in mammals. The gene for the PTC taste receptor, TAS2R38, was identified in 2003. Polymerase Chain Reaction (PCR) is used to amplify a sho ...
... Bitter-tasting compounds are recognized by receptor proteins on the surface of taste cells. There are approximately 30 genes for different bitter taste receptors in mammals. The gene for the PTC taste receptor, TAS2R38, was identified in 2003. Polymerase Chain Reaction (PCR) is used to amplify a sho ...
Transposable Elements in Rice Plants
... forms of retroviruses. Two general methods have been developed to isolate retrotransposon of plants. By using these methods, at least 12 families of retrotransposons of rice (Tosl-Tosl2) were isolated. One retrotransposon, Tos3-1, was subjected to detailed investigation. Tos3-1 is 5.2 kb long and ha ...
... forms of retroviruses. Two general methods have been developed to isolate retrotransposon of plants. By using these methods, at least 12 families of retrotransposons of rice (Tosl-Tosl2) were isolated. One retrotransposon, Tos3-1, was subjected to detailed investigation. Tos3-1 is 5.2 kb long and ha ...
LDheatmap (Version 0.9-1): Example of Adding Tracks
... > load(system.file("extdata/addTracks.RData",package="LDheatmap")) The object GIMAP5.CEU is is a list with two elements: snp.data and snp.support. snp.data is a snp.matrix object from the chopsticks package, containing the SNP genotypes. Rows correspond to subjects and columns correspond to SNPs. sn ...
... > load(system.file("extdata/addTracks.RData",package="LDheatmap")) The object GIMAP5.CEU is is a list with two elements: snp.data and snp.support. snp.data is a snp.matrix object from the chopsticks package, containing the SNP genotypes. Rows correspond to subjects and columns correspond to SNPs. sn ...
Document
... has become a primary model for social behavior Complex social behavior in controllable urban environment Normal Behavior – honey bees live in the wild Controllable Environment – hives can be modified Small size manageable with current genomic technology Capture bees on-the-fly during normal behavior ...
... has become a primary model for social behavior Complex social behavior in controllable urban environment Normal Behavior – honey bees live in the wild Controllable Environment – hives can be modified Small size manageable with current genomic technology Capture bees on-the-fly during normal behavior ...
Primer design - ILRI Research Computing
... higher specificity and gives you space to add restriction enzyme sites to the primer end for cloning. 2. Make sure the melting temperature (Tm) of the primers used are not more than 5°C different from each other. You can calculate Tm with this formula: Tm = 4(G + C) + 2(A + T)°C 3. Aim for a Tm betw ...
... higher specificity and gives you space to add restriction enzyme sites to the primer end for cloning. 2. Make sure the melting temperature (Tm) of the primers used are not more than 5°C different from each other. You can calculate Tm with this formula: Tm = 4(G + C) + 2(A + T)°C 3. Aim for a Tm betw ...
Comparison of the separation of Candida albicans chromosome
... gel, run under conditions similar to those in Figure 1, but on which the largest chromosomes are better resolved (25). The 8 bands visible in Figure 2A were designated as letters A - H on the basis of hybridization to a cloned genomic DNA probe specific to a given band. A chromosome nomenclature bas ...
... gel, run under conditions similar to those in Figure 1, but on which the largest chromosomes are better resolved (25). The 8 bands visible in Figure 2A were designated as letters A - H on the basis of hybridization to a cloned genomic DNA probe specific to a given band. A chromosome nomenclature bas ...
software development and application in bioinformatics: single
... This thesis incorporates two projects, one in assessing software availability and application in detecting SNPs for next generation sequencing, and the other in software engineering of a social networking environment for use in biomedical informatics. SNP Detection: The study on variations in DNA se ...
... This thesis incorporates two projects, one in assessing software availability and application in detecting SNPs for next generation sequencing, and the other in software engineering of a social networking environment for use in biomedical informatics. SNP Detection: The study on variations in DNA se ...
SNP Discovery and Genotyping Workshop (PowerPoint)
... Taqman Genotyping with fluorescence-based homogenous assays (single-tube assay) = 1 SNP/ tube ...
... Taqman Genotyping with fluorescence-based homogenous assays (single-tube assay) = 1 SNP/ tube ...
Somatic Mutations in HLA Genes - ASHI-U
... Alternatively, these might be random mutations in “fragile” ...
... Alternatively, these might be random mutations in “fragile” ...
View PDF
... amplify CCTG repeats in the first intron of CCHC-type zinc finger, nucleic acid binding protein (CNBP) gene on chromosome 3q21 as a primary screening of myotonic dystrophy type 2 (DM2)11. The PCR was performed using GeneAmp PCR System 9700 (Applied Biosystems, USA) in a 50 μl mixture. The primers we ...
... amplify CCTG repeats in the first intron of CCHC-type zinc finger, nucleic acid binding protein (CNBP) gene on chromosome 3q21 as a primary screening of myotonic dystrophy type 2 (DM2)11. The PCR was performed using GeneAmp PCR System 9700 (Applied Biosystems, USA) in a 50 μl mixture. The primers we ...
Genome organization of Magnaporthe grisea
... A cosmid library of genomic DNA from strain 2539 cloned in pMLF1 (Leong et al. 1994) was assayed by colony hybridization with MAGGY internal regions as probes (Farman et al. 1997b), and 57 MAGGY-hybridizing clones were identified in approximately 3500 cosmids screened. The cosmid DNAs were purified ...
... A cosmid library of genomic DNA from strain 2539 cloned in pMLF1 (Leong et al. 1994) was assayed by colony hybridization with MAGGY internal regions as probes (Farman et al. 1997b), and 57 MAGGY-hybridizing clones were identified in approximately 3500 cosmids screened. The cosmid DNAs were purified ...
Geuvadis Analysis Meeting
... could be explainable by allele-specific expression ~4000 cases where DNA is homozygous and RNA not (!!!) remove FPs from computational or experimental artifacts (PCR artifacts?) ...
... could be explainable by allele-specific expression ~4000 cases where DNA is homozygous and RNA not (!!!) remove FPs from computational or experimental artifacts (PCR artifacts?) ...
XistAR write up
... to our understanding of X-inactivation via Xist thus far, these researchers found an additional novel piece of long non-coding RNA expressed from the inactivated X chromosome. They identified this lncRNA to be antisense of Xist, and that its expression is required for proper Xist functioning. Here, ...
... to our understanding of X-inactivation via Xist thus far, these researchers found an additional novel piece of long non-coding RNA expressed from the inactivated X chromosome. They identified this lncRNA to be antisense of Xist, and that its expression is required for proper Xist functioning. Here, ...
Chromosomes - WordPress.com
... The fluorescently labeled probe of interest is then added to the denatured sample mixture and hybridizes with the sample DNA at the target site as it reanneals (or reforms itself) back into a double helix. The probe signal can then be seen through a fluorescent microscope and the sample DNA scor ...
... The fluorescently labeled probe of interest is then added to the denatured sample mixture and hybridizes with the sample DNA at the target site as it reanneals (or reforms itself) back into a double helix. The probe signal can then be seen through a fluorescent microscope and the sample DNA scor ...
Molecular Inversion Probe
Molecular Inversion Probe (MIP) belongs to the class of Capture by Circularization molecular techniques for performing genomic partitioning, a process through which one captures and enriches specific regions of the genome. Probes used in this technique are single stranded DNA molecules and, similar to other genomic partitioning techniques, contain sequences that are complementary to the target in the genome; these probes hybridize to and capture the genomic target. MIP stands unique from other genomic partitioning strategies in that MIP probes share the common design of two genomic target complementary segments separated by a linker region. With this design, when the probe hybridizes to the target, it undergoes an inversion in configuration (as suggested by the name of the technique) and circularizes. Specifically, the two target complementary regions at the 5’ and 3’ ends of the probe become adjacent to one another while the internal linker region forms a free hanging loop. The technology has been used extensively in the HapMap project for large-scale SNP genotyping as well as for studying gene copy alterationsand characteristics of specific genomic loci to identify biomarkers for different diseases such as cancer. Key strengths of the MIP technology include its high specificity to the target and its scalability for high-throughput, multiplexed analyses where tens of thousands of genomic loci are assayed simultaneously.