Structured Review

Promega rsa i
Diagrammatic representation of the TMDH process. (A) A library of transposon mutants is obtained using a custom transposon with outward-facing T7 and SP6 promoters. Genomic <t>DNA</t> is extracted from the library and digested using a restriction endonuclease ( Rsa I). Labelled RNA run-offs are obtained from the T7 and SP6 promoters by in vitro transcription. (B) The labelled RNA run-offs are hybridised to genome-wide tiling microarrays. By examining the distribution of microarray signals between <t>Rsa</t> I restriction sites (vertical black lines) it is possible to infer the location of the transposon (green triangle). Comparison of the library grown in vitro (input) with the library obtained after passage through a mouse (output) allows attenuating mutants to be identified, since they give lower signals in the output.
Rsa I, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice"

Article Title: Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1000529

Diagrammatic representation of the TMDH process. (A) A library of transposon mutants is obtained using a custom transposon with outward-facing T7 and SP6 promoters. Genomic DNA is extracted from the library and digested using a restriction endonuclease ( Rsa I). Labelled RNA run-offs are obtained from the T7 and SP6 promoters by in vitro transcription. (B) The labelled RNA run-offs are hybridised to genome-wide tiling microarrays. By examining the distribution of microarray signals between Rsa I restriction sites (vertical black lines) it is possible to infer the location of the transposon (green triangle). Comparison of the library grown in vitro (input) with the library obtained after passage through a mouse (output) allows attenuating mutants to be identified, since they give lower signals in the output.
Figure Legend Snippet: Diagrammatic representation of the TMDH process. (A) A library of transposon mutants is obtained using a custom transposon with outward-facing T7 and SP6 promoters. Genomic DNA is extracted from the library and digested using a restriction endonuclease ( Rsa I). Labelled RNA run-offs are obtained from the T7 and SP6 promoters by in vitro transcription. (B) The labelled RNA run-offs are hybridised to genome-wide tiling microarrays. By examining the distribution of microarray signals between Rsa I restriction sites (vertical black lines) it is possible to infer the location of the transposon (green triangle). Comparison of the library grown in vitro (input) with the library obtained after passage through a mouse (output) allows attenuating mutants to be identified, since they give lower signals in the output.

Techniques Used: In Vitro, Genome Wide, Microarray

Related Articles

Clone Assay:

Article Title: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant
Article Snippet: Regions were scored as CNVs if the log2 ratio of ⩾2 consecutive clones each exceeded 2×SD of the autosomal clones in dye-swap replicate experiments. .. In brief, genomic DNAs from the patient and from a single sex-matched reference patient were separately double-digested using the restriction endonucleases Alu I and Rsa I (Promega, Leiden, The Netherlands) and purified using Microcon centrifugal filter devices (Millipore Corporation, Missouri, Minneapolis, USA).

Amplification:

Article Title: Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification
Article Snippet: .. Before labeling, we assessed the DNA yield with a NanoDrop Spectrophotometer (Thermo Fisher Scientific) and forwarded the required amount of DNA for restriction enzyme digestion with Alu I and Rsa I (Promega) at 37 °C for 2 h. We then used the BioPrime DNA Labeling System (Invitrogen) to label 300 ng of the amplified sample DNA (single cells) and “low cell” reference DNA (obtained from 10 cells of normal cultured lymphocytes). .. Random primers (octamers) were annealed to the denatured DNA template and extended with Klenow fragment in the presence of biotin-16-dUTP (Roche Diagnostics) for sample DNA and digoxigenin-11-dUTP (Roche Diagnostics) for reference DNA.

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array. .. Changes in test DNA copy number at specific loci were considered only if they were < −0.38 (deletion) or > 0.38 (amplification) of the log2 ratio values from at least five consecutive probes.

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: .. Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ). ..

Article Title: Crohn’s disease in Japanese is associated with a SNP-haplotype of N-acetyltransferase 2 gene
Article Snippet: Amplification protocol comprised initial denaturation at 94 °C for 5 min; 35 cycles of denaturation at 94 °C for 30 s, annealing at 55 °C for 30 s, and extension at 72 °C for 30 s; and a final extension at 72 °C for 5 min. PCR products were used for DHPLC analysis. .. After digestion of PCR products by Rsa I (Promega, WI, USA), the fragments were subjected to electrophoresis on 2% agarose gel, and visualized as described above.

Article Title: Association of the Apolipoprotein E 2 Allele with Concurrent Occurrence of Endometrial Hyperplasia and Endometrial Carcinoma
Article Snippet: .. Amplified fragments were digested with either Rsa I (Promega, Madison, WI, USA) or BclI (SIGMA, Saint Louis, MO, USA) for detection of the Cys282Tyr or His63Asp of the HFE gene; Cfo (Promega, Madison, WI, USA) for the APOE genotype determination and Hsp92II (Promega, Madison, WI, USA) for the Val158Met of the COMT gene. .. PCR products and digested fragments were run on 8% polyacrylamide gels, stained with ethidium bromide, and visualized by UV.

Article Title: A Rapid PCR-Based DNA Test for Enterotoxic Bacillus cereus
Article Snippet: .. The hemolysin amplification fragment was digested with Rsa I, Taq I, and Xba I (all from Promega). .. 16S rDNA RFLP analyses were performed on 56 strains with Cfo I, Hae III, Msp I, and Rsa I (all from Promega).

Blocking Assay:

Article Title: Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Article Snippet: Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega), and purified with the QIAprep Spin Miniprep kit (Qiagen). .. Test DNA (500 ng) and reference DNA (500 ng) l were labeled with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Bioprime Array CGH Genomic Labeling kit (Invitrogen), and hybridized with 2× Hybridization buffer (Agilent, Palo Alto, CA), 10× blocking agent (Agilent,), and Human Cot-1 DNA (Invitrogen) in an Agilent SureHyb chamber for 24 hours at 65°C.

Article Title: Crohn’s disease in Japanese is associated with a SNP-haplotype of N-acetyltransferase 2 gene
Article Snippet: SNPs at codons 129 and 131 lying in a linkage disequilibrium (LD) block were detected by PCR-denaturing high-performance liquid chromatography (DHPLC) with an automated HPLC instrument (WAVETM , Transgenomic, CA, USA), and by direct DNA sequencing with ABI 310 (Applied Biosystems, Foster City, USA). .. After digestion of PCR products by Rsa I (Promega, WI, USA), the fragments were subjected to electrophoresis on 2% agarose gel, and visualized as described above.

Electrophoresis:

Article Title: Crohn’s disease in Japanese is associated with a SNP-haplotype of N-acetyltransferase 2 gene
Article Snippet: .. After digestion of PCR products by Rsa I (Promega, WI, USA), the fragments were subjected to electrophoresis on 2% agarose gel, and visualized as described above. ..

Article Title: A Rapid PCR-Based DNA Test for Enterotoxic Bacillus cereus
Article Snippet: The hemolysin amplification fragment was digested with Rsa I, Taq I, and Xba I (all from Promega). .. Further analysis of the gel results was done with the Gelcompar program package (GelCompar, comparative analysis of electrophoresis patterns version 4.0; Applied Maths, Kortrijk, Belgium).

Microarray:

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: By comparing the ratio of two different fluorescence signals at each target spot in the microarray, CNVs are detected in specific sequences or genes between two genomes (Gijsbers et al., 2011; Shoukier et al., 2013). .. For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array.

Article Title: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant
Article Snippet: In brief, genomic DNAs from the patient and from a single sex-matched reference patient were separately double-digested using the restriction endonucleases Alu I and Rsa I (Promega, Leiden, The Netherlands) and purified using Microcon centrifugal filter devices (Millipore Corporation, Missouri, Minneapolis, USA). .. The hybridised arrays were washed and scanned (Microarray Scanner; Agilent).

Article Title: Distinct Genetic Alterations in Colorectal Cancer
Article Snippet: An oligo microarray-based CGH using a chip containing 105,000 human probes (Agilent, Santa Clara, CA) was used. .. Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD).

Article Title: High-throughput marker discovery in melon using a self-designed oligo microarray
Article Snippet: .. Microarray labeling, hybridization and scanning gDNA (2.5 μg) was digested with restriction enzymes Alu I and Rsa I (Promega, USA). .. The digested DNA was used for labeling and hybridization following Agilent procedures for CGH [ ].

Article Title: Aneuploidy as a mechanism for stress-induced liver adaptation
Article Snippet: Array CGH was performed using Agilent 180K SurePrint G3 Mouse Microarray (cat. no. G4826A-027411, NCBI Build 37) with 1.8 kb overall median probe spacing. .. Briefly, 1 μg of genomic DNA from test (i.e., hepatocytes) and 1 μg of reference (i.e., splenocytes) samples were digested with Alu I and Rsa I (Promega) at 37°C for 2 hours and labeled by cyanine 5-dCTP (for the test sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer) at 37°C for 2 hours using the Bioprime CGH Labeling Module (Invitrogen).

Article Title: Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Article Snippet: Restriction digests and in vitro transcription 10 µg of genomic DNA from each TMDH input and output pool, and from the untransposed control DNA, was digested using Rsa I (Promega) overnight at 37°C. .. Equal amounts of digested DNA from 2 or 3 pools of mutants were combined to give 8 sets of 960–1440 mutants each for microarray analysis (see ).

Genome Wide:

Article Title: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant
Article Snippet: An additional patient with a 16p13.11 duplication was identified by array CGH to human 105K genome-wide oligonucleotide arrays (Agilent Technologies, Diegem, Belgium) according to the manufacturer’s instructions. .. In brief, genomic DNAs from the patient and from a single sex-matched reference patient were separately double-digested using the restriction endonucleases Alu I and Rsa I (Promega, Leiden, The Netherlands) and purified using Microcon centrifugal filter devices (Millipore Corporation, Missouri, Minneapolis, USA).

Derivative Assay:

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: Primers were derived from the published sequence of S. aureus agr group II strain N315 (GenBank accession number AP003135 ; bp 277870 to 277890 [primer S1], bp 279014 to 278997 [primer S2], bp 280043 to 280063 [primer S3], and bp 281219 to 281199 [primer S4]) ( ). .. Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

Hybridization:

Article Title: Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion
Article Snippet: For each aCGH experiment, 400 ng each of purified DNA and normal sex-matched DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8 × 60 K commercial arrays (Agilent). .. After hybridization, the arrays were scanned using a dual-laser scanner (Agilent) and the images were extracted and analyzed using Feature Extraction software (Agilent) and Workbench genomics software, respectively.

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: aCGH analysis aCGH is a specific array-based genomic hybridization method that uses different fluorescent dyes to label DNA from patients and controls, to identify differences between the two groups (Sealfon and Chu, 2011; Brady and Vermeesch, 2012). .. For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array.

Article Title: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant
Article Snippet: Paragraph title: Array comparative genome hybridisation ... In brief, genomic DNAs from the patient and from a single sex-matched reference patient were separately double-digested using the restriction endonucleases Alu I and Rsa I (Promega, Leiden, The Netherlands) and purified using Microcon centrifugal filter devices (Millipore Corporation, Missouri, Minneapolis, USA).

Article Title: Genetic effects of a 13q31.1 microdeletion detected by noninvasive prenatal testing (NIPT)
Article Snippet: Paragraph title: Array-based comparative genomic hybridization ... As previously described, for each aCGH experiment, 400 ng of purified DNA and normal sex-matched DNA (BioChain Institute, Inc.) were digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI, USA) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8×60 K commercial arrays (Agilent).

Article Title: Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Article Snippet: Paragraph title: Comparative genomic hybridization (CGH) ... Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega), and purified with the QIAprep Spin Miniprep kit (Qiagen).

Article Title: High-throughput marker discovery in melon using a self-designed oligo microarray
Article Snippet: .. Microarray labeling, hybridization and scanning gDNA (2.5 μg) was digested with restriction enzymes Alu I and Rsa I (Promega, USA). .. The digested DNA was used for labeling and hybridization following Agilent procedures for CGH [ ].

Article Title: A rare de novo duplication of chromosome 21q22.12 → q22.3 with other concomitant deletion and duplication of small fragments in 21q associated with Down syndrome: Prenatal diagnosis, molecular cytogenetic characterization
Article Snippet: For each aCGH experiment, 400 ng of genomic DNA and normal female DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). .. After hybridization, the arrays were scanned using a dual-laser scanner (Agilent) and the images were extracted and analyzed using Feature Extraction software (Agilent) and Workbench genomics software, respectively.

Article Title: Aneuploidy as a mechanism for stress-induced liver adaptation
Article Snippet: DNA digestion, labeling, and hybridization were performed according to the manufacturer’s instructions, with slight modifications as described ( ). .. Briefly, 1 μg of genomic DNA from test (i.e., hepatocytes) and 1 μg of reference (i.e., splenocytes) samples were digested with Alu I and Rsa I (Promega) at 37°C for 2 hours and labeled by cyanine 5-dCTP (for the test sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer) at 37°C for 2 hours using the Bioprime CGH Labeling Module (Invitrogen).

High Performance Liquid Chromatography:

Article Title: Crohn’s disease in Japanese is associated with a SNP-haplotype of N-acetyltransferase 2 gene
Article Snippet: SNPs at codons 129 and 131 lying in a linkage disequilibrium (LD) block were detected by PCR-denaturing high-performance liquid chromatography (DHPLC) with an automated HPLC instrument (WAVETM , Transgenomic, CA, USA), and by direct DNA sequencing with ABI 310 (Applied Biosystems, Foster City, USA). .. After digestion of PCR products by Rsa I (Promega, WI, USA), the fragments were subjected to electrophoresis on 2% agarose gel, and visualized as described above.

Cell Culture:

Article Title: Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification
Article Snippet: .. Before labeling, we assessed the DNA yield with a NanoDrop Spectrophotometer (Thermo Fisher Scientific) and forwarded the required amount of DNA for restriction enzyme digestion with Alu I and Rsa I (Promega) at 37 °C for 2 h. We then used the BioPrime DNA Labeling System (Invitrogen) to label 300 ng of the amplified sample DNA (single cells) and “low cell” reference DNA (obtained from 10 cells of normal cultured lymphocytes). .. Random primers (octamers) were annealed to the denatured DNA template and extended with Klenow fragment in the presence of biotin-16-dUTP (Roche Diagnostics) for sample DNA and digoxigenin-11-dUTP (Roche Diagnostics) for reference DNA.

Generated:

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: 1.9 kb containing agrB , agrD , and agrC were generated as recently described ( ). .. Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

DNA Sequencing:

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: Paragraph title: PCR, restriction fragment length polymorphism (RFLP) analysis, and DNA sequencing of the agr locus. ... Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

Article Title: Crohn’s disease in Japanese is associated with a SNP-haplotype of N-acetyltransferase 2 gene
Article Snippet: SNPs at codons 129 and 131 lying in a linkage disequilibrium (LD) block were detected by PCR-denaturing high-performance liquid chromatography (DHPLC) with an automated HPLC instrument (WAVETM , Transgenomic, CA, USA), and by direct DNA sequencing with ABI 310 (Applied Biosystems, Foster City, USA). .. After digestion of PCR products by Rsa I (Promega, WI, USA), the fragments were subjected to electrophoresis on 2% agarose gel, and visualized as described above.

DNA Labeling:

Article Title: Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification
Article Snippet: .. Before labeling, we assessed the DNA yield with a NanoDrop Spectrophotometer (Thermo Fisher Scientific) and forwarded the required amount of DNA for restriction enzyme digestion with Alu I and Rsa I (Promega) at 37 °C for 2 h. We then used the BioPrime DNA Labeling System (Invitrogen) to label 300 ng of the amplified sample DNA (single cells) and “low cell” reference DNA (obtained from 10 cells of normal cultured lymphocytes). .. Random primers (octamers) were annealed to the denatured DNA template and extended with Klenow fragment in the presence of biotin-16-dUTP (Roche Diagnostics) for sample DNA and digoxigenin-11-dUTP (Roche Diagnostics) for reference DNA.

Article Title: Distinct Genetic Alterations in Colorectal Cancer
Article Snippet: Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD). .. Test DNA (1.5 µg) and reference DNA (1.5 µg; Promega) were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus.

Sequencing:

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: Primers were derived from the published sequence of S. aureus agr group II strain N315 (GenBank accession number AP003135 ; bp 277870 to 277890 [primer S1], bp 279014 to 278997 [primer S2], bp 280043 to 280063 [primer S3], and bp 281219 to 281199 [primer S4]) ( ). .. Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

DNA Extraction:

Article Title: Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion
Article Snippet: Total DNA was extracted from uncultured CVS tissues with a commercially available Genomic DNA Extraction Kit (BioChain Institute Inc., Newark, CA) according to the manufacturer's instructions. .. For each aCGH experiment, 400 ng each of purified DNA and normal sex-matched DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8 × 60 K commercial arrays (Agilent).

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: Total DNA was extracted from peripheral whole blood using a commercially available DNA-isolation kit (BioChain Inc., Beijing, China), according to the manufacturer's protocol. .. For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array.

Article Title: Genetic effects of a 13q31.1 microdeletion detected by noninvasive prenatal testing (NIPT)
Article Snippet: Total genomic DNA was extracted from 10 ml of fetal amniotic fluid or 2 ml of uncultured venous blood samples from the parents with a commercially available Amniotic Fluid Genomic DNA Extraction Kit and a Blood Genomic DNA Extraction kit, respectively (both from BioChain Institute Inc., Newark, CA), according to the manufacturer’s instructions. .. As previously described, for each aCGH experiment, 400 ng of purified DNA and normal sex-matched DNA (BioChain Institute, Inc.) were digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI, USA) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8×60 K commercial arrays (Agilent).

Article Title: A rare de novo duplication of chromosome 21q22.12 → q22.3 with other concomitant deletion and duplication of small fragments in 21q associated with Down syndrome: Prenatal diagnosis, molecular cytogenetic characterization
Article Snippet: aCGH analysis Genomic DNA was extracted from 10 ml of amniotic fluid with a commercially available Amniotic Fluid Genomic DNA Extraction Kit (BioChain Institute Inc., Newark, CA) according to the manufacturer's instructions. .. For each aCGH experiment, 400 ng of genomic DNA and normal female DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA).

Nucleic Acid Electrophoresis:

Article Title: A Rapid PCR-Based DNA Test for Enterotoxic Bacillus cereus
Article Snippet: The hemolysin amplification fragment was digested with Rsa I, Taq I, and Xba I (all from Promega). .. The digested PCR products were run at 200 V for 5.5 h in 5% agarose gels (0.5× TAE buffer) containing (0.25 mg/ml) ethidium bromide by using a water-cooled gel electrophoresis apparatus (SuperSub; Hoefer Scientific Instruments, San Francisco, Calif.).

Fluorescence:

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: By comparing the ratio of two different fluorescence signals at each target spot in the microarray, CNVs are detected in specific sequences or genes between two genomes (Gijsbers et al., 2011; Shoukier et al., 2013). .. For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array.

Isolation:

Article Title: Aneuploidy as a mechanism for stress-induced liver adaptation
Article Snippet: Genomic DNA from hepatocyte and splenocyte samples was isolated using DNeasy Blood and Tissue Kit (QIAGEN). .. Briefly, 1 μg of genomic DNA from test (i.e., hepatocytes) and 1 μg of reference (i.e., splenocytes) samples were digested with Alu I and Rsa I (Promega) at 37°C for 2 hours and labeled by cyanine 5-dCTP (for the test sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer) at 37°C for 2 hours using the Bioprime CGH Labeling Module (Invitrogen).

Labeling:

Article Title: Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification
Article Snippet: .. Before labeling, we assessed the DNA yield with a NanoDrop Spectrophotometer (Thermo Fisher Scientific) and forwarded the required amount of DNA for restriction enzyme digestion with Alu I and Rsa I (Promega) at 37 °C for 2 h. We then used the BioPrime DNA Labeling System (Invitrogen) to label 300 ng of the amplified sample DNA (single cells) and “low cell” reference DNA (obtained from 10 cells of normal cultured lymphocytes). .. Random primers (octamers) were annealed to the denatured DNA template and extended with Klenow fragment in the presence of biotin-16-dUTP (Roche Diagnostics) for sample DNA and digoxigenin-11-dUTP (Roche Diagnostics) for reference DNA.

Article Title: Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion
Article Snippet: .. For each aCGH experiment, 400 ng each of purified DNA and normal sex-matched DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8 × 60 K commercial arrays (Agilent). ..

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: .. For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array. ..

Article Title: Distinct Genetic Alterations in Colorectal Cancer
Article Snippet: Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD). .. Test DNA (1.5 µg) and reference DNA (1.5 µg; Promega) were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus.

Article Title: Genetic effects of a 13q31.1 microdeletion detected by noninvasive prenatal testing (NIPT)
Article Snippet: .. As previously described, for each aCGH experiment, 400 ng of purified DNA and normal sex-matched DNA (BioChain Institute, Inc.) were digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI, USA) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8×60 K commercial arrays (Agilent). ..

Article Title: Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Article Snippet: Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega), and purified with the QIAprep Spin Miniprep kit (Qiagen). .. Test DNA (500 ng) and reference DNA (500 ng) l were labeled with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Bioprime Array CGH Genomic Labeling kit (Invitrogen), and hybridized with 2× Hybridization buffer (Agilent, Palo Alto, CA), 10× blocking agent (Agilent,), and Human Cot-1 DNA (Invitrogen) in an Agilent SureHyb chamber for 24 hours at 65°C.

Article Title: High-throughput marker discovery in melon using a self-designed oligo microarray
Article Snippet: .. Microarray labeling, hybridization and scanning gDNA (2.5 μg) was digested with restriction enzymes Alu I and Rsa I (Promega, USA). .. The digested DNA was used for labeling and hybridization following Agilent procedures for CGH [ ].

Article Title: A rare de novo duplication of chromosome 21q22.12 → q22.3 with other concomitant deletion and duplication of small fragments in 21q associated with Down syndrome: Prenatal diagnosis, molecular cytogenetic characterization
Article Snippet: .. For each aCGH experiment, 400 ng of genomic DNA and normal female DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). .. The aCGH analysis was performed using 8 × 60 K commercial arrays (Agilent).

Article Title: Aneuploidy as a mechanism for stress-induced liver adaptation
Article Snippet: .. Briefly, 1 μg of genomic DNA from test (i.e., hepatocytes) and 1 μg of reference (i.e., splenocytes) samples were digested with Alu I and Rsa I (Promega) at 37°C for 2 hours and labeled by cyanine 5-dCTP (for the test sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer) at 37°C for 2 hours using the Bioprime CGH Labeling Module (Invitrogen). .. Labeled DNA of the test samples and gender-mismatched Microarray image files were quantified using Agilent Feature Extraction software (version 9.5), and text file outputs were imported into Agilent Genomic Workbench software (version 6.5).

Purification:

Article Title: Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification
Article Snippet: The purified samples were recovered from the spin columns with 30 μ L of water. .. Before labeling, we assessed the DNA yield with a NanoDrop Spectrophotometer (Thermo Fisher Scientific) and forwarded the required amount of DNA for restriction enzyme digestion with Alu I and Rsa I (Promega) at 37 °C for 2 h. We then used the BioPrime DNA Labeling System (Invitrogen) to label 300 ng of the amplified sample DNA (single cells) and “low cell” reference DNA (obtained from 10 cells of normal cultured lymphocytes).

Article Title: Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion
Article Snippet: .. For each aCGH experiment, 400 ng each of purified DNA and normal sex-matched DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8 × 60 K commercial arrays (Agilent). ..

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: .. For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array. ..

Article Title: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant
Article Snippet: .. In brief, genomic DNAs from the patient and from a single sex-matched reference patient were separately double-digested using the restriction endonucleases Alu I and Rsa I (Promega, Leiden, The Netherlands) and purified using Microcon centrifugal filter devices (Millipore Corporation, Missouri, Minneapolis, USA). .. Then 1.5 μg of the digested products were differentially labelled by random priming with Cy3-dUTP and Cy5-dUTP (Perkin Elmer, Foster City, California, USA) and cohybridised to the array for 48 hrs at 65°C in a rotating oven.

Article Title: Distinct Genetic Alterations in Colorectal Cancer
Article Snippet: .. Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD). .. Test DNA (1.5 µg) and reference DNA (1.5 µg; Promega) were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus.

Article Title: Genetic effects of a 13q31.1 microdeletion detected by noninvasive prenatal testing (NIPT)
Article Snippet: .. As previously described, for each aCGH experiment, 400 ng of purified DNA and normal sex-matched DNA (BioChain Institute, Inc.) were digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI, USA) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8×60 K commercial arrays (Agilent). ..

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: PCR products were purified for RFLP and DNA sequencing by using Microcon centrifugal devices (Millipore Corp., Bedford, Mass.) as recommended by the manufacturer. .. Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

Article Title: Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Article Snippet: .. Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega), and purified with the QIAprep Spin Miniprep kit (Qiagen). .. Test DNA (500 ng) and reference DNA (500 ng) l were labeled with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Bioprime Array CGH Genomic Labeling kit (Invitrogen), and hybridized with 2× Hybridization buffer (Agilent, Palo Alto, CA), 10× blocking agent (Agilent,), and Human Cot-1 DNA (Invitrogen) in an Agilent SureHyb chamber for 24 hours at 65°C.

Article Title: Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Article Snippet: Restriction digests and in vitro transcription 10 µg of genomic DNA from each TMDH input and output pool, and from the untransposed control DNA, was digested using Rsa I (Promega) overnight at 37°C. .. Digested DNA was cleaned using a Qiagen QIAquick PCR Purification Kit and eluted in 30 µl RNase-free water (Qiagen).

Polymerase Chain Reaction:

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: Paragraph title: PCR, restriction fragment length polymorphism (RFLP) analysis, and DNA sequencing of the agr locus. ... Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

Article Title: Crohn’s disease in Japanese is associated with a SNP-haplotype of N-acetyltransferase 2 gene
Article Snippet: .. After digestion of PCR products by Rsa I (Promega, WI, USA), the fragments were subjected to electrophoresis on 2% agarose gel, and visualized as described above. ..

Article Title: Association of the Apolipoprotein E 2 Allele with Concurrent Occurrence of Endometrial Hyperplasia and Endometrial Carcinoma
Article Snippet: PCR-reactions were carried out as follows: at first 15 min denaturing at 95°C and then 30 amplification cycles (30 s at 94°C, 30 s at 67°C, 1 min at 72°C) for APOE ; 30 cycles (30 s at 94°C, 1 min at 60°C, 30 s at 72°C) for HFE ; and 40 cycles (30 s at 94°C, 1 min at 57°C, 30 s at 72°C) for COMT . .. Amplified fragments were digested with either Rsa I (Promega, Madison, WI, USA) or BclI (SIGMA, Saint Louis, MO, USA) for detection of the Cys282Tyr or His63Asp of the HFE gene; Cfo (Promega, Madison, WI, USA) for the APOE genotype determination and Hsp92II (Promega, Madison, WI, USA) for the Val158Met of the COMT gene.

Article Title: A Rapid PCR-Based DNA Test for Enterotoxic Bacillus cereus
Article Snippet: The hemolysin amplification fragment was digested with Rsa I, Taq I, and Xba I (all from Promega). .. The digested PCR products were run at 200 V for 5.5 h in 5% agarose gels (0.5× TAE buffer) containing (0.25 mg/ml) ethidium bromide by using a water-cooled gel electrophoresis apparatus (SuperSub; Hoefer Scientific Instruments, San Francisco, Calif.).

Article Title: Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Article Snippet: Restriction digests and in vitro transcription 10 µg of genomic DNA from each TMDH input and output pool, and from the untransposed control DNA, was digested using Rsa I (Promega) overnight at 37°C. .. Digested DNA was cleaned using a Qiagen QIAquick PCR Purification Kit and eluted in 30 µl RNase-free water (Qiagen).

Chromatin Immunoprecipitation:

Article Title: Distinct Genetic Alterations in Colorectal Cancer
Article Snippet: An oligo microarray-based CGH using a chip containing 105,000 human probes (Agilent, Santa Clara, CA) was used. .. Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD).

Software:

Article Title: Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion
Article Snippet: For each aCGH experiment, 400 ng each of purified DNA and normal sex-matched DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). aCGH analysis was performed using 8 × 60 K commercial arrays (Agilent). .. After hybridization, the arrays were scanned using a dual-laser scanner (Agilent) and the images were extracted and analyzed using Feature Extraction software (Agilent) and Workbench genomics software, respectively.

Article Title: Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis
Article Snippet: For each aCGH experiment, purified DNA and normal sex-matched DNA (1 µg each; Promega, Madison, WI, USA) were digested with Alu I and Rsa I (10 U each; Promega), and differentially labelled with cyanine-5 and cyanine-3 fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA, USA). aCGH analysis was performed using the Agilent 8 × 60K commercial array. .. After hybridization, arrays were scanned using a dual-laser scanner (Agilent), and images extracted and analyzed using the Feature Extraction (Agilent) and Workbench genomics software, respectively.

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ). .. Sequence data was analyzed by using EDITSEQ and MEGALIGN software (DNASTAR, Inc., Madison, Wis.).

Article Title: Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Article Snippet: Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega), and purified with the QIAprep Spin Miniprep kit (Qiagen). .. Raw data were obtained by Agilent Feature extraction software 9.0, and then imported into Agilent CGH analytics 3.5 software for analysis.

Article Title: A rare de novo duplication of chromosome 21q22.12 → q22.3 with other concomitant deletion and duplication of small fragments in 21q associated with Down syndrome: Prenatal diagnosis, molecular cytogenetic characterization
Article Snippet: For each aCGH experiment, 400 ng of genomic DNA and normal female DNA (BioChain Institute) was digested with 10 U Alu I and 10 U Rsa I (Promega, Madison, WI) and differentially labeled with cyanine-5 (cy5) and cyanine-3 (Cy3) fluorescent dyes using a Genomic DNA Enzymatic Labeling Kit (Agilent, Santa Clara, CA). .. After hybridization, the arrays were scanned using a dual-laser scanner (Agilent) and the images were extracted and analyzed using Feature Extraction software (Agilent) and Workbench genomics software, respectively.

Article Title: Aneuploidy as a mechanism for stress-induced liver adaptation
Article Snippet: Briefly, 1 μg of genomic DNA from test (i.e., hepatocytes) and 1 μg of reference (i.e., splenocytes) samples were digested with Alu I and Rsa I (Promega) at 37°C for 2 hours and labeled by cyanine 5-dCTP (for the test sample) or cyanine 3-dCTP (for the reference sample) (PerkinElmer) at 37°C for 2 hours using the Bioprime CGH Labeling Module (Invitrogen). .. Labeled DNA of the test samples and gender-mismatched Microarray image files were quantified using Agilent Feature Extraction software (version 9.5), and text file outputs were imported into Agilent Genomic Workbench software (version 6.5).

DNA Hybridization:

Article Title: Distinct Genetic Alterations in Colorectal Cancer
Article Snippet: Briefly, the test and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD). .. Following probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65°C with rotation for 40 hr at 20 rpm.

Agarose Gel Electrophoresis:

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: DNA fragments were separated by 1% agarose gel electrophoresis and then visualized under UV light after they were stained with ethidium bromide. .. Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

Article Title: Crohn’s disease in Japanese is associated with a SNP-haplotype of N-acetyltransferase 2 gene
Article Snippet: .. After digestion of PCR products by Rsa I (Promega, WI, USA), the fragments were subjected to electrophoresis on 2% agarose gel, and visualized as described above. ..

In Vitro:

Article Title: Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Article Snippet: .. Restriction digests and in vitro transcription 10 µg of genomic DNA from each TMDH input and output pool, and from the untransposed control DNA, was digested using Rsa I (Promega) overnight at 37°C. .. Digested DNA was cleaned using a Qiagen QIAquick PCR Purification Kit and eluted in 30 µl RNase-free water (Qiagen).

Spectrophotometry:

Article Title: Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification
Article Snippet: .. Before labeling, we assessed the DNA yield with a NanoDrop Spectrophotometer (Thermo Fisher Scientific) and forwarded the required amount of DNA for restriction enzyme digestion with Alu I and Rsa I (Promega) at 37 °C for 2 h. We then used the BioPrime DNA Labeling System (Invitrogen) to label 300 ng of the amplified sample DNA (single cells) and “low cell” reference DNA (obtained from 10 cells of normal cultured lymphocytes). .. Random primers (octamers) were annealed to the denatured DNA template and extended with Klenow fragment in the presence of biotin-16-dUTP (Roche Diagnostics) for sample DNA and digoxigenin-11-dUTP (Roche Diagnostics) for reference DNA.

Article Title: Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Article Snippet: Restriction digests and in vitro transcription 10 µg of genomic DNA from each TMDH input and output pool, and from the untransposed control DNA, was digested using Rsa I (Promega) overnight at 37°C. .. The DNA concentration and A260 /A280 ratio were measured on a NanoDrop 1000 spectrophotometer.

Concentration Assay:

Article Title: Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Article Snippet: Restriction digests and in vitro transcription 10 µg of genomic DNA from each TMDH input and output pool, and from the untransposed control DNA, was digested using Rsa I (Promega) overnight at 37°C. .. The DNA concentration and A260 /A280 ratio were measured on a NanoDrop 1000 spectrophotometer.

Standard Deviation:

Article Title: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant
Article Snippet: Regions were scored as CNVs if one clone passed the threshold of 4× the normal standard deviation (SD), and if ⩾2 flanking clones passed the threshold of log2 (3/2)−2×SD. .. In brief, genomic DNAs from the patient and from a single sex-matched reference patient were separately double-digested using the restriction endonucleases Alu I and Rsa I (Promega, Leiden, The Netherlands) and purified using Microcon centrifugal filter devices (Millipore Corporation, Missouri, Minneapolis, USA).

Staining:

Article Title: Accessory Gene Regulator (agr) Locus in Geographically Diverse Staphylococcus aureus Isolates with Reduced Susceptibility to Vancomycin
Article Snippet: DNA fragments were separated by 1% agarose gel electrophoresis and then visualized under UV light after they were stained with ethidium bromide. .. Alu I and Rsa I (Promega) were used to perform RFLP analyses of agrB-agrD-agrC amplification products ( ).

Article Title: Association of the Apolipoprotein E 2 Allele with Concurrent Occurrence of Endometrial Hyperplasia and Endometrial Carcinoma
Article Snippet: Amplified fragments were digested with either Rsa I (Promega, Madison, WI, USA) or BclI (SIGMA, Saint Louis, MO, USA) for detection of the Cys282Tyr or His63Asp of the HFE gene; Cfo (Promega, Madison, WI, USA) for the APOE genotype determination and Hsp92II (Promega, Madison, WI, USA) for the Val158Met of the COMT gene. .. PCR products and digested fragments were run on 8% polyacrylamide gels, stained with ethidium bromide, and visualized by UV.

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  • 92
    Promega rsa i
    Diagrams representing restriction patterns of 16S rRNA gene digested with Dde I ( a ), Hha I ( b ) or <t>Rsa</t> I ( c ). First column in each diagram corresponds to the banding pattern for the 1 Kb ladder
    Rsa I, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rsa i/product/Promega
    Average 92 stars, based on 39 article reviews
    Price from $9.99 to $1999.99
    rsa i - by Bioz Stars, 2020-02
    92/100 stars
      Buy from Supplier

    80
    Promega endonuclease rsa i
    The kDNA <t>PCR</t> and RFLP products of the 12 Palestinian L. tropica strains. a , The kDNA PCR products of three of the 12 Palestinian strains: LRC-L890, -L891, -L887, and reference strains of L. tropica , -L758, and L. major , -L137; MW: molecular weight marker ΦX174 DNA/Hinf; b , The RFLP patterns of the six different genotypes resulting from digestion of kDNA PCR products with Rsa I. MW: molecular weight marker ΦX174 DNA/HaeIII Markers; c , Dendrogram based on the kDNA restriction fragment length polymorphism (RFLP) of the strains of L. tropica after digestion of their PCR products, separately, with the endonucleases <t>Rsa</t> I and Mbo I, which yielded ten sub-genotypes that segregated into the Clade A, with kDNA sub-type Ltro -kD1 and the Clade B, with kDNA sub-type Ltro -kD2. It was constructed using RAPDistance Package (version 1.04) and was based on the presence or absence of the bands in each sample. The numbers on the branches represent the % of difference. The lengths of the branches indicate the degree of similarity in fingerprints among the strains of L. tropica relative to the strain of L. major , MHOM/IL/67/JerichoII (=LRC-L137), which served as an out-group in this analysis: Ts = Tubas; Ma = Meselya; Yn = El-Yamoon; Jn = Jenin; S-h = Silat El hartheyia; Tb = Tiberias; KA = Kfar Adumim. The zymodemal designations and EF serotypes are given for complete comparison.
    Endonuclease Rsa I, supplied by Promega, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/endonuclease rsa i/product/Promega
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    endonuclease rsa i - by Bioz Stars, 2020-02
    80/100 stars
      Buy from Supplier

    Image Search Results


    Diagrams representing restriction patterns of 16S rRNA gene digested with Dde I ( a ), Hha I ( b ) or Rsa I ( c ). First column in each diagram corresponds to the banding pattern for the 1 Kb ladder

    Journal: Microbial ecology

    Article Title: Characterization of the Bacterial Diversity in Indo-West Pacific Loliginid and Sepiolid Squid Light Organs

    doi: 10.1007/s00248-012-0099-6

    Figure Lengend Snippet: Diagrams representing restriction patterns of 16S rRNA gene digested with Dde I ( a ), Hha I ( b ) or Rsa I ( c ). First column in each diagram corresponds to the banding pattern for the 1 Kb ladder

    Article Snippet: RFLP analysis was completed as described by Urakawa et al. [ , ] using three restriction endonucleases: Rsa I (5′GTAC3′), Hha I (5′GCGC3′) and Dde I (5′CTNAG3′; Promega Corporation, Madison, WI).

    Techniques:

    Plasmid map of pCS36-4CPA with restriction sites of the endonucleases Alu I, Kzo 9I and Rsa I. The regions transcribed as RNAI and RNAII are shown as green arrows. The single-strand initiation site ( ssi ) and multimer resolution site ( mrs ) are coloured in pink and yellow, respectively. The mobilisation machinery genes are depicted as red arrows. The open reading frames ORF5, ORF6 and ORF7 are shown as unpainted arrows. Abbreviations: oriV , origin of replication; oriT , origin of transfer; nic , sequence-specific cleavage site.

    Journal: Saudi Journal of Biological Sciences

    Article Title: Isolation and sequence analysis of pCS36-4CPA, a small plasmid from Citrobacter sp. 36-4CPA

    doi: 10.1016/j.sjbs.2016.02.014

    Figure Lengend Snippet: Plasmid map of pCS36-4CPA with restriction sites of the endonucleases Alu I, Kzo 9I and Rsa I. The regions transcribed as RNAI and RNAII are shown as green arrows. The single-strand initiation site ( ssi ) and multimer resolution site ( mrs ) are coloured in pink and yellow, respectively. The mobilisation machinery genes are depicted as red arrows. The open reading frames ORF5, ORF6 and ORF7 are shown as unpainted arrows. Abbreviations: oriV , origin of replication; oriT , origin of transfer; nic , sequence-specific cleavage site.

    Article Snippet: Later, Kzo 9I, Rsa I and Alu I fragments were cloned into pGEM-3Zf(+) (Promega).

    Techniques: Plasmid Preparation, Sequencing

    kDNA restriction fragment length polymorphisms (RFLPs) of Leishmania infantum chagasi strains digested with either Hpa II or Rsa I, and separated by gel electrophoresis on 3% Metaphor agarose. Samples are in the same lane for both gels. From left to right:

    Journal: The American Journal of Tropical Medicine and Hygiene

    Article Title: Heterogeneity of Leishmania infantum chagasi Kinetoplast DNA in Teresina (Brazil)

    doi: 10.4269/ajtmh.2010.09-0600

    Figure Lengend Snippet: kDNA restriction fragment length polymorphisms (RFLPs) of Leishmania infantum chagasi strains digested with either Hpa II or Rsa I, and separated by gel electrophoresis on 3% Metaphor agarose. Samples are in the same lane for both gels. From left to right:

    Article Snippet: After the procedure, pellets were rinsed in 10 μL of water and 5 μL were used for endonuclease digestion for 2 h using either Rsa I or Hpa II in enzyme buffer (Promega, Madison, WI), according to the manufacturer's recommendations.

    Techniques: Nucleic Acid Electrophoresis

    The kDNA PCR and RFLP products of the 12 Palestinian L. tropica strains. a , The kDNA PCR products of three of the 12 Palestinian strains: LRC-L890, -L891, -L887, and reference strains of L. tropica , -L758, and L. major , -L137; MW: molecular weight marker ΦX174 DNA/Hinf; b , The RFLP patterns of the six different genotypes resulting from digestion of kDNA PCR products with Rsa I. MW: molecular weight marker ΦX174 DNA/HaeIII Markers; c , Dendrogram based on the kDNA restriction fragment length polymorphism (RFLP) of the strains of L. tropica after digestion of their PCR products, separately, with the endonucleases Rsa I and Mbo I, which yielded ten sub-genotypes that segregated into the Clade A, with kDNA sub-type Ltro -kD1 and the Clade B, with kDNA sub-type Ltro -kD2. It was constructed using RAPDistance Package (version 1.04) and was based on the presence or absence of the bands in each sample. The numbers on the branches represent the % of difference. The lengths of the branches indicate the degree of similarity in fingerprints among the strains of L. tropica relative to the strain of L. major , MHOM/IL/67/JerichoII (=LRC-L137), which served as an out-group in this analysis: Ts = Tubas; Ma = Meselya; Yn = El-Yamoon; Jn = Jenin; S-h = Silat El hartheyia; Tb = Tiberias; KA = Kfar Adumim. The zymodemal designations and EF serotypes are given for complete comparison.

    Journal: Parasites & Vectors

    Article Title: Genetic, serological and biochemical characterization of Leishmania tropica from foci in northern Palestine and discovery of zymodeme MON-307

    doi: 10.1186/1756-3305-5-121

    Figure Lengend Snippet: The kDNA PCR and RFLP products of the 12 Palestinian L. tropica strains. a , The kDNA PCR products of three of the 12 Palestinian strains: LRC-L890, -L891, -L887, and reference strains of L. tropica , -L758, and L. major , -L137; MW: molecular weight marker ΦX174 DNA/Hinf; b , The RFLP patterns of the six different genotypes resulting from digestion of kDNA PCR products with Rsa I. MW: molecular weight marker ΦX174 DNA/HaeIII Markers; c , Dendrogram based on the kDNA restriction fragment length polymorphism (RFLP) of the strains of L. tropica after digestion of their PCR products, separately, with the endonucleases Rsa I and Mbo I, which yielded ten sub-genotypes that segregated into the Clade A, with kDNA sub-type Ltro -kD1 and the Clade B, with kDNA sub-type Ltro -kD2. It was constructed using RAPDistance Package (version 1.04) and was based on the presence or absence of the bands in each sample. The numbers on the branches represent the % of difference. The lengths of the branches indicate the degree of similarity in fingerprints among the strains of L. tropica relative to the strain of L. major , MHOM/IL/67/JerichoII (=LRC-L137), which served as an out-group in this analysis: Ts = Tubas; Ma = Meselya; Yn = El-Yamoon; Jn = Jenin; S-h = Silat El hartheyia; Tb = Tiberias; KA = Kfar Adumim. The zymodemal designations and EF serotypes are given for complete comparison.

    Article Snippet: The PCR product was digested separately with either the endonuclease Rsa I or Mbo I (Promega, Madison, WI), according to the manufacturer’s instructions. kDNA of L. tropica ISER/IL/98/LRC-L758 was included as a positive reference and that of L. major MHOM/IL/67/JerichoII (=LRC-L137) as the out-group. kDNA-RFLP results were analyzed using the RAPDistance Package version 1.04 ( http://www.anu.edu.au/Bozo/software/ ).

    Techniques: Polymerase Chain Reaction, Molecular Weight, Marker, Construct