genomic dna fragments  (Thermo Fisher)


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    Name:
    DNAzol Reagent for isolation of genomic DNA from solid and liquid samples
    Description:
    DNAzol Reagent is a complete and ready to use organic reagent for the isolation of genomic DNA from solid and liquid samples of animal plant yeast and bacterial origin The DNAzol Reagent procedure can be completed in typically 10 30 minutes with DNA recoveries of 70 100 DNAzol Reagent is • Versatile can use with a broad spectrum of sample materials• Efficient rapid isolation and high recovery of genomic DNAEfficient isolation of genomic DNA from a variety of sample typesThe DNAzol Reagent procedure uses a novel guanidine detergent lysing solution that permits selective precipitation of DNA from cell lysate 1 mL of DNAzol Reagent can be used to isolate genomic DNA from 1 3 x 107 cells from 0 1 mL of whole blood or from 25 50 mg tissue Rapid isolation and high recovery of genomic DNAThe DNAzol Reagent combines reliability efficiency and simplicity in its DNA isolation protocol During isolation a biological sample is lysed or homogenized in DNAzol Reagent and the genomic DNA is then precipitated from the lysate with ethanol Following an ethanol wash DNA may be solubilized in either water or 8 mM NaOH The entire procedure can be completed in 10 30 min with DNA recovery of 70 100 Isolated DNA can be used for a number of downstream applicationsGenomic DNA extracted using the DNAzol procedure is suitable for a variety of applications including Southern blotting cloning PCR restriction endonuclease digestion and dot blot hybridization
    Catalog Number:
    10503027
    Price:
    None
    Category:
    Kits and Assays
    Applications:
    DNA & RNA Purification & Analysis|DNA Extraction|Genomic DNA Purification|gDNA from Animal Tissues & Cells
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    Structured Review

    Thermo Fisher genomic dna fragments
    Electrophoretograms of PCR products resulting from amplification of T. <t>spiralis</t> and T. pseudospiralis genomic <t>DNA,</t> performed with primers specific for the ends of T. spiralis thymidylate synthase ORF. The accurate lengths, based on sequencing, are given for T. spiralis and T. pseudospiralis (in parentheses) genes, and for T. pseudospiralis retrogene.
    DNAzol Reagent is a complete and ready to use organic reagent for the isolation of genomic DNA from solid and liquid samples of animal plant yeast and bacterial origin The DNAzol Reagent procedure can be completed in typically 10 30 minutes with DNA recoveries of 70 100 DNAzol Reagent is • Versatile can use with a broad spectrum of sample materials• Efficient rapid isolation and high recovery of genomic DNAEfficient isolation of genomic DNA from a variety of sample typesThe DNAzol Reagent procedure uses a novel guanidine detergent lysing solution that permits selective precipitation of DNA from cell lysate 1 mL of DNAzol Reagent can be used to isolate genomic DNA from 1 3 x 107 cells from 0 1 mL of whole blood or from 25 50 mg tissue Rapid isolation and high recovery of genomic DNAThe DNAzol Reagent combines reliability efficiency and simplicity in its DNA isolation protocol During isolation a biological sample is lysed or homogenized in DNAzol Reagent and the genomic DNA is then precipitated from the lysate with ethanol Following an ethanol wash DNA may be solubilized in either water or 8 mM NaOH The entire procedure can be completed in 10 30 min with DNA recovery of 70 100 Isolated DNA can be used for a number of downstream applicationsGenomic DNA extracted using the DNAzol procedure is suitable for a variety of applications including Southern blotting cloning PCR restriction endonuclease digestion and dot blot hybridization
    https://www.bioz.com/result/genomic dna fragments/product/Thermo Fisher
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    genomic dna fragments - by Bioz Stars, 2021-04
    97/100 stars

    Images

    1) Product Images from "Trichinella pseudospiralis vs. T. spiralis thymidylate synthase gene structure and T. pseudospiralis thymidylate synthase retrogene sequence"

    Article Title: Trichinella pseudospiralis vs. T. spiralis thymidylate synthase gene structure and T. pseudospiralis thymidylate synthase retrogene sequence

    Journal: Parasites & Vectors

    doi: 10.1186/1756-3305-7-175

    Electrophoretograms of PCR products resulting from amplification of T. spiralis and T. pseudospiralis genomic DNA, performed with primers specific for the ends of T. spiralis thymidylate synthase ORF. The accurate lengths, based on sequencing, are given for T. spiralis and T. pseudospiralis (in parentheses) genes, and for T. pseudospiralis retrogene.
    Figure Legend Snippet: Electrophoretograms of PCR products resulting from amplification of T. spiralis and T. pseudospiralis genomic DNA, performed with primers specific for the ends of T. spiralis thymidylate synthase ORF. The accurate lengths, based on sequencing, are given for T. spiralis and T. pseudospiralis (in parentheses) genes, and for T. pseudospiralis retrogene.

    Techniques Used: Polymerase Chain Reaction, Amplification, Sequencing

    2) Product Images from "Histone demethylase Lsd1 is required for the differentiation of neural cells in the cnidarian Nematostella vectensis"

    Article Title: Histone demethylase Lsd1 is required for the differentiation of neural cells in the cnidarian Nematostella vectensis

    Journal: bioRxiv

    doi: 10.1101/2020.09.07.285577

    NvLsd1 is ubiquitously expressed but developmentally regulated. ( A ) Reduced phylogeny showing the position of the 4 non-bilaterian animal lineages with respect to the Bilateria. The evolution of animal multicellularity is annotated by a blue star and the lineages possessing a nervous system are marked with a red circle. Phylogeny based on ( 39 ). ( B ) Schematic showing the strategy for generating the NvLsd1 GFP knock-in allele by CRISPR-Cas9 mediated homologous recombination. ( C-H ) Confocal images of immunofluorescence staining on NvLsd1 GFP animals. Stage is shown on the left. Oral is shown to the right in F-H. NvLsd1-GFP is shown in green, DNA in blue and F-Actin in magenta. F-H show mid-lateral views. ( I-L ) Close ups of NvLsd1-GFP in the ectoderm at different stages. Scale bars: 50 μm (C-H), 20 μm (I-L).
    Figure Legend Snippet: NvLsd1 is ubiquitously expressed but developmentally regulated. ( A ) Reduced phylogeny showing the position of the 4 non-bilaterian animal lineages with respect to the Bilateria. The evolution of animal multicellularity is annotated by a blue star and the lineages possessing a nervous system are marked with a red circle. Phylogeny based on ( 39 ). ( B ) Schematic showing the strategy for generating the NvLsd1 GFP knock-in allele by CRISPR-Cas9 mediated homologous recombination. ( C-H ) Confocal images of immunofluorescence staining on NvLsd1 GFP animals. Stage is shown on the left. Oral is shown to the right in F-H. NvLsd1-GFP is shown in green, DNA in blue and F-Actin in magenta. F-H show mid-lateral views. ( I-L ) Close ups of NvLsd1-GFP in the ectoderm at different stages. Scale bars: 50 μm (C-H), 20 μm (I-L).

    Techniques Used: Knock-In, CRISPR, Homologous Recombination, Immunofluorescence, Staining

    Lsd1 mutants have major defects in cnidocyte differentiation. ( A, B ) Confocal images of immunofluorescence staining on control and NvLsd1 −/− late planula showing DNA in blue, mature cnidocysts in green and NvNcol3 in magenta. ( C ) Quantification of mature DAPI + cnidocysts from control and NvLsd1 −/− late planula. The number of cnidocysts in a 100 μM section in the center of each larva was counted. Statistical significance was calculated using a Student’s t-test. ( D, E ) Close ups of the regions highlighted in A’ ( D ) and B’ ( E ) showing NvNcol3 staining in grey. ( F, G ) Confocal images of Immunofluorescence staining on control and NvLsd1 −/− primary polyps. DNA is shown in blue, mature cnidocysts in green and NvNcol3 in magenta. ( H, I ) High magnification of NvNcol3 staining in the tentacles of primary polyps in F ( H ) and G ( I ) showing NvNcol3 staining in grey. Scale bars: 50 μm (A, B, F and G), 20 μm (D, E) and 10 μm (H, I).
    Figure Legend Snippet: Lsd1 mutants have major defects in cnidocyte differentiation. ( A, B ) Confocal images of immunofluorescence staining on control and NvLsd1 −/− late planula showing DNA in blue, mature cnidocysts in green and NvNcol3 in magenta. ( C ) Quantification of mature DAPI + cnidocysts from control and NvLsd1 −/− late planula. The number of cnidocysts in a 100 μM section in the center of each larva was counted. Statistical significance was calculated using a Student’s t-test. ( D, E ) Close ups of the regions highlighted in A’ ( D ) and B’ ( E ) showing NvNcol3 staining in grey. ( F, G ) Confocal images of Immunofluorescence staining on control and NvLsd1 −/− primary polyps. DNA is shown in blue, mature cnidocysts in green and NvNcol3 in magenta. ( H, I ) High magnification of NvNcol3 staining in the tentacles of primary polyps in F ( H ) and G ( I ) showing NvNcol3 staining in grey. Scale bars: 50 μm (A, B, F and G), 20 μm (D, E) and 10 μm (H, I).

    Techniques Used: Immunofluorescence, Staining

    NvLsd1 is required cell autonomously for cnidocyte differentiation ( A-C ) Immunostaining on NvLsd1 −/− animals injected with NvPOU4 :NvLsd1-mCherry ( A ), NvPOU4 :NvH2B-mCherry ( B ) or NvPOU4 :NvLsd1 K644A/A520E -mCherry ( C ). DNA is shown in blue, DAPI + cnidocysts in green and mCherry in magenta. Scale bars: 10 μm.
    Figure Legend Snippet: NvLsd1 is required cell autonomously for cnidocyte differentiation ( A-C ) Immunostaining on NvLsd1 −/− animals injected with NvPOU4 :NvLsd1-mCherry ( A ), NvPOU4 :NvH2B-mCherry ( B ) or NvPOU4 :NvLsd1 K644A/A520E -mCherry ( C ). DNA is shown in blue, DAPI + cnidocysts in green and mCherry in magenta. Scale bars: 10 μm.

    Techniques Used: Immunostaining, Injection

    NvLsd1 is highly expressed in differentiated neural cells. ( A ) Confocal images showing close up of the ectoderm of NvLsd1 GFP late gastrula treated with Edu for 4 hours stained with anti-GFP antibody (green) and Click-IT Edu (Magenta). DNA is shown in blue. ( B-E ) Confocal images of immunofluorescence staining on late planula of NvLsd1 GFP animals crossed with NvElav1 ::mOrange ( B ), NvFoxQ2d ::mOrange ( C ), NvNcol3 ::mOrange2 ( D ) and mid-planula crossed with NvPTx1 ::mOrange2 ( E ) transgenics. DNA is shown in blue, GFP in green and mOrange in magenta. ( F ) Histograms of flow cytometry data on Lsd GFP animals crossed to the indicated transgenic lines. The X-axis shows the GFP fluoresce levels (units are arbitrary) and the Y-axis shows the cell number normalized to mode to correct for the different numbers of cells in the mOrange + and mOrange − gates. Scale bars: 20 μm.
    Figure Legend Snippet: NvLsd1 is highly expressed in differentiated neural cells. ( A ) Confocal images showing close up of the ectoderm of NvLsd1 GFP late gastrula treated with Edu for 4 hours stained with anti-GFP antibody (green) and Click-IT Edu (Magenta). DNA is shown in blue. ( B-E ) Confocal images of immunofluorescence staining on late planula of NvLsd1 GFP animals crossed with NvElav1 ::mOrange ( B ), NvFoxQ2d ::mOrange ( C ), NvNcol3 ::mOrange2 ( D ) and mid-planula crossed with NvPTx1 ::mOrange2 ( E ) transgenics. DNA is shown in blue, GFP in green and mOrange in magenta. ( F ) Histograms of flow cytometry data on Lsd GFP animals crossed to the indicated transgenic lines. The X-axis shows the GFP fluoresce levels (units are arbitrary) and the Y-axis shows the cell number normalized to mode to correct for the different numbers of cells in the mOrange + and mOrange − gates. Scale bars: 20 μm.

    Techniques Used: Staining, Immunofluorescence, Flow Cytometry, Transgenic Assay

    3) Product Images from "Molecular mechanisms governing Pcdh-? gene expression: Evidence for a multiple promoter and cis-alternative splicing model"

    Article Title: Molecular mechanisms governing Pcdh-? gene expression: Evidence for a multiple promoter and cis-alternative splicing model

    Journal: Genes & Development

    doi: 10.1101/gad.1004802

    Individual Pcdh -γ variable exons have their own promoters. ( A ) Identification of SNPs and RFLPs in variable exon B6 between 129S and CBA/J mouse strains. The relevant sequences from different mouse strains are shown as well as SspI RFLP analysis of genomic DNA from different mouse strains. ( B ) Targeting of a B6 transgene from the CBA/J strain into the Pcdh -γ locus in mouse ES cells (129S strain). The CBA/J B6 transgene consists of 2.5-kb 5′ flanking sequence, the coding exon and 2.1 kb of intronic sequence. This transgene is transcribed in the same orientation as the endogenous Pcdh -γ gene cluster. cDNA RFLP analysis revealed that the CBA/J-B6 exon was expressed at a level similar to the endogenous 129S-B6 exon (lanes 1,3 ). Wild-type ES cells serve as a control (lane 5 ). The RT (minus) control excludes the possibility of genomic DNA contamination.
    Figure Legend Snippet: Individual Pcdh -γ variable exons have their own promoters. ( A ) Identification of SNPs and RFLPs in variable exon B6 between 129S and CBA/J mouse strains. The relevant sequences from different mouse strains are shown as well as SspI RFLP analysis of genomic DNA from different mouse strains. ( B ) Targeting of a B6 transgene from the CBA/J strain into the Pcdh -γ locus in mouse ES cells (129S strain). The CBA/J B6 transgene consists of 2.5-kb 5′ flanking sequence, the coding exon and 2.1 kb of intronic sequence. This transgene is transcribed in the same orientation as the endogenous Pcdh -γ gene cluster. cDNA RFLP analysis revealed that the CBA/J-B6 exon was expressed at a level similar to the endogenous 129S-B6 exon (lanes 1,3 ). Wild-type ES cells serve as a control (lane 5 ). The RT (minus) control excludes the possibility of genomic DNA contamination.

    Techniques Used: Crocin Bleaching Assay, Sequencing

    A single Pcdh-γ allele expresses multiple variable exons. ( A ) DNA recombination model for Pcdh ). ( B ) Detection of multiple different Pcdh -γ genes using single-cell RT-PCR. Single neurons from Pcdh -γ del/GFP cerebellum (postnatal P5) were used to detect γC-GFP, A12-γC, A11-γC, and B2-γC.
    Figure Legend Snippet: A single Pcdh-γ allele expresses multiple variable exons. ( A ) DNA recombination model for Pcdh ). ( B ) Detection of multiple different Pcdh -γ genes using single-cell RT-PCR. Single neurons from Pcdh -γ del/GFP cerebellum (postnatal P5) were used to detect γC-GFP, A12-γC, A11-γC, and B2-γC.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction

    Cis -splicing in the absence of upstream sequence from constant exon 1. ( A ) Deletion of C5 and conserved upstream DNA sequences from constant exon 1. A 5-kb sequence containing the entire C5 gene and the conserved DNA sequences upstream of constant exon 1 was deleted by gene targeting in ES cells carrying only one Pcdh -γ allele. ( B ) RT-PCR analysis showed that individual variable exons (C3, C4, B2, B6, and A12) were efficiently spliced to γ constant exons in the absence of the 5-kb upstream sequence from constant exon 1.
    Figure Legend Snippet: Cis -splicing in the absence of upstream sequence from constant exon 1. ( A ) Deletion of C5 and conserved upstream DNA sequences from constant exon 1. A 5-kb sequence containing the entire C5 gene and the conserved DNA sequences upstream of constant exon 1 was deleted by gene targeting in ES cells carrying only one Pcdh -γ allele. ( B ) RT-PCR analysis showed that individual variable exons (C3, C4, B2, B6, and A12) were efficiently spliced to γ constant exons in the absence of the 5-kb upstream sequence from constant exon 1.

    Techniques Used: Sequencing, Reverse Transcription Polymerase Chain Reaction

    4) Product Images from "Gene cloning, sequence analysis, and expression of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase"

    Article Title: Gene cloning, sequence analysis, and expression of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi:

    Construction of pPC1 expression plasmid. ( A ) Plasmid pBluMH. The thin line indicates the plasmid region derived from pBluescript vector, the empty box indicates the probe area. Number in parenthesis indicates the length of DNA (in kb) with reference to the Pst I site near T3 promoter as the origin point. MHPCO gene ( B ) was isolated from pBluMH by PCR and ligated to pET-11a ( C ), resulting in the expression plasmid pPC1 ( D ). The mark indicates the length representing 1,000 nucleotides.
    Figure Legend Snippet: Construction of pPC1 expression plasmid. ( A ) Plasmid pBluMH. The thin line indicates the plasmid region derived from pBluescript vector, the empty box indicates the probe area. Number in parenthesis indicates the length of DNA (in kb) with reference to the Pst I site near T3 promoter as the origin point. MHPCO gene ( B ) was isolated from pBluMH by PCR and ligated to pET-11a ( C ), resulting in the expression plasmid pPC1 ( D ). The mark indicates the length representing 1,000 nucleotides.

    Techniques Used: Expressing, Plasmid Preparation, Derivative Assay, Isolation, Polymerase Chain Reaction, Positron Emission Tomography

    5) Product Images from "Selective Elimination of Osteosarcoma Cell Lines with Short Telomeres by ATR Inhibitors"

    Article Title: Selective Elimination of Osteosarcoma Cell Lines with Short Telomeres by ATR Inhibitors

    Journal: bioRxiv

    doi: 10.1101/2020.08.18.254664

    Characterisation of Telomere Status in Osteosarcoma Cell Lines a) C-Circle Assay (CCA) Level . Graph shows the CCA level calculated by subtracting the phi-29 polymerase NTC by the phi-29 polymerase free control NTC (see methods). A sample is then considered ALT+ if its CCA level lower error bar is > 0. Data is represented as a mean of three independent experiments. Error bars show standard deviation. Dot blot result of phi-29 polymerase is shown in Supplementary Figure 1a. b) APB Assay for the osteosarcoma cell lines with long telomeres . APBs were scored as a direct co-localisation between TRF2 and PML foci. The graph shows the mean percentage of cells containing 0, 1 or > 1 APBs in their nuclei for three independently prepared samples of > 50 cells. Error bars show standard deviation. c) Representative immunofluorescence images showing the presence/absence of APBs in the KPD and MHM cell lines respectively. TRF2 was stained green and PML bodies were stained red. Yellow foci (co-localisation of green and red foci) in the merge panel represent APBs. A 50-μm scale bar is shown. Representative images of all tested cell lines are shown in Supplementary Figure 2. d) Telomere Southern blot of osteosarcoma cell lines . Terminal restriction fragment length analysis of genomic DNA digested with Hin fI and Rsa I and hybridised with a telomeric TTAGGG probe. ALT-negative cell lines tend to have shorter telomeres than HEK293T, while ALT-positive cell lines tend to have longer telomeres than HEK293T, which are extremely heterogeneous in length. Digital analysis of telomere length is shown in Table 1 .
    Figure Legend Snippet: Characterisation of Telomere Status in Osteosarcoma Cell Lines a) C-Circle Assay (CCA) Level . Graph shows the CCA level calculated by subtracting the phi-29 polymerase NTC by the phi-29 polymerase free control NTC (see methods). A sample is then considered ALT+ if its CCA level lower error bar is > 0. Data is represented as a mean of three independent experiments. Error bars show standard deviation. Dot blot result of phi-29 polymerase is shown in Supplementary Figure 1a. b) APB Assay for the osteosarcoma cell lines with long telomeres . APBs were scored as a direct co-localisation between TRF2 and PML foci. The graph shows the mean percentage of cells containing 0, 1 or > 1 APBs in their nuclei for three independently prepared samples of > 50 cells. Error bars show standard deviation. c) Representative immunofluorescence images showing the presence/absence of APBs in the KPD and MHM cell lines respectively. TRF2 was stained green and PML bodies were stained red. Yellow foci (co-localisation of green and red foci) in the merge panel represent APBs. A 50-μm scale bar is shown. Representative images of all tested cell lines are shown in Supplementary Figure 2. d) Telomere Southern blot of osteosarcoma cell lines . Terminal restriction fragment length analysis of genomic DNA digested with Hin fI and Rsa I and hybridised with a telomeric TTAGGG probe. ALT-negative cell lines tend to have shorter telomeres than HEK293T, while ALT-positive cell lines tend to have longer telomeres than HEK293T, which are extremely heterogeneous in length. Digital analysis of telomere length is shown in Table 1 .

    Techniques Used: Standard Deviation, Dot Blot, Immunofluorescence, Staining, Southern Blot

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    Article Title: Midkine drives cardiac inflammation by promoting neutrophil trafficking and NETosis in myocarditis
    Article Snippet: RNA isolation and real-time PCR Hearts of EAM or sham-treated control mice were removed, rinsed with PBS, and homogenized mechanically using an Ultra-Turrax T8 homogenizer (IKA Labortechnik). .. RNA was isolated using TRIzol (15596026; Thermo Fisher) according to the manufacturer’s protocol, and genomic DNA was digested using the DNase I Amplification Grade kit (18068015; Thermo Fisher). .. 1 µg total RNA was transcribed into cDNA using the Omniscript RT kit (205111; Qiagen).

    Amplification:

    Article Title: Midkine drives cardiac inflammation by promoting neutrophil trafficking and NETosis in myocarditis
    Article Snippet: RNA isolation and real-time PCR Hearts of EAM or sham-treated control mice were removed, rinsed with PBS, and homogenized mechanically using an Ultra-Turrax T8 homogenizer (IKA Labortechnik). .. RNA was isolated using TRIzol (15596026; Thermo Fisher) according to the manufacturer’s protocol, and genomic DNA was digested using the DNase I Amplification Grade kit (18068015; Thermo Fisher). .. 1 µg total RNA was transcribed into cDNA using the Omniscript RT kit (205111; Qiagen).

    Picogreen Assay:

    Article Title: Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis
    Article Snippet: .. Genomic DNA was extracted from ESCC samples by the standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies). ..

    Polymerase Chain Reaction:

    Article Title: Functional Characterization of FLT3 Receptor Signaling Deregulation in Acute Myeloid Leukemia by Single Cell Network Profiling (SCNP)
    Article Snippet: .. For the analysis of internal tandem duplication of the FLT3 receptor gene, PCR was performed on 500 ng genomic DNA using published primers 11F and 12R as described to identify ITD insertions in the JM and TK1 domains using AmpliTaq Gold DNA polymerase (Applied Biosystems) and 3% agarose gels. .. For samples with no available genomic DNA, the PCR assay was performed with 100 ng of cDNA prepared using the High Capacity RNA-to cDNA kit (Applied Biosystems).

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    Thermo Fisher genomic short dna
    <t>DNA-PK</t> kinase activity inhibition by synthesized short DNA fragments. Recombinant p53 protein was incubated with DNA-PK in the presence of <t>γ-</t> 32 P-ATP and various lengths of DNA: synthesized double-stranded oligos (14 mer, 20 mer, 24 mer, 28 mer,
    Genomic Short Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genomic short dna/product/Thermo Fisher
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    99
    Thermo Fisher genomic dna fragments
    Multiple sequence alignments of <t>cDNA</t> and genomic <t>DNA</t> amplicons amplified from 10 low and high/very high seed weight homozygous RIL mapping individuals, parental genotypes (ICC 4958 and ICC 17163), and 12 contrasting germplasm lines using the two seed weight-regulating differentially expressed CNMS marker-associated LOB-domain proten- (A) and KANADI protein-encoding (B) genes validated the presence of microsatellite repeat motifs. The presence of variable CNMS repeat units, such as (GA) n and (CAA) n , in the signal sequence-binding sites of the GAGA8HVBKN3 and RAV1AAT regulatory elements of these two genes, respectively, which differentiated all of the low seed weight germplasm lines, parents, and homozygous mapping individuals (amplifying 158bp and 150bp alleles) from the high/very high seed weight germplasm lines, parents, and homozygous RILs (160/162bp and 156bp alleles) was evident. HSL, homozygous lines. (This figure is available in colour at JXB online.)
    Genomic Dna Fragments, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Price from $9.99 to $1999.99
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    Thermo Fisher abi 3130 genetic analyzer
    Characterization of SMA haplotypes. (A) To characterize the extent of SMN1 deletions, we performed PCR on loci that mapped to multiple sites in the region. By selecting amplicons which exhibited sequence changes between loci, we were able to assess the presence or absence of each locus after PCR amplification and Sanger sequencing. Green blocks represent loci that were present, and red blocks denote deleted loci. The samples (i.e. haplotype combinations) are listed on the left side of the figure. (B) Competitive PCR was used to calculate SMN2 copy number in our patient cohort. Samples were subjected to multiplex PCR with limiting deoxynucleotide triphosphates and the resulting amplicons were size-fractionated on an <t>ABI</t> 3130 Genetic Analyzer. Samples with greater SMN2 copy number demonstrated increased generation of SMN2 -specific product versus an internal control locus (albumin gene, ALB ). (C) The area under the curve for each amplicon, as provided by the Sequencing Analysis software, was used to calculate the ratio of SMN2 -specific product to ALB product. For SMN2 copy number from 1–4, three separate samples were PCR amplified and analyzed, and the SMN2/ALB ratios were highly correlated with SMN2 copy number.
    Abi 3130 Genetic Analyzer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    DNA-PK kinase activity inhibition by synthesized short DNA fragments. Recombinant p53 protein was incubated with DNA-PK in the presence of γ- 32 P-ATP and various lengths of DNA: synthesized double-stranded oligos (14 mer, 20 mer, 24 mer, 28 mer,

    Journal: Journal of radiation research

    Article Title: Radiation-generated short DNA fragments may perturb non-homologous end-joining and induce genomic instability

    doi:

    Figure Lengend Snippet: DNA-PK kinase activity inhibition by synthesized short DNA fragments. Recombinant p53 protein was incubated with DNA-PK in the presence of γ- 32 P-ATP and various lengths of DNA: synthesized double-stranded oligos (14 mer, 20 mer, 24 mer, 28 mer,

    Article Snippet: Genomic short DNA (20-400 bp) fragments generated by γ-ray or neutrons were introduced to MCF-10A cells by using lipofectin according to the manufacture's instructions (Invitrogen).

    Techniques: Activity Assay, Inhibition, Synthesized, Recombinant, Incubation

    Sample AFM images of pUC19 DNA irradiated to 10 kGy Co-60 γ-photon (Panel A) and 390 MeV/nucleon Argon ion (Panel B) and the corresponding fragment size distributions (Panel C). The fragment size distributions were obtained by measuring the length

    Journal: Journal of radiation research

    Article Title: Radiation-generated short DNA fragments may perturb non-homologous end-joining and induce genomic instability

    doi:

    Figure Lengend Snippet: Sample AFM images of pUC19 DNA irradiated to 10 kGy Co-60 γ-photon (Panel A) and 390 MeV/nucleon Argon ion (Panel B) and the corresponding fragment size distributions (Panel C). The fragment size distributions were obtained by measuring the length

    Article Snippet: Genomic short DNA (20-400 bp) fragments generated by γ-ray or neutrons were introduced to MCF-10A cells by using lipofectin according to the manufacture's instructions (Invitrogen).

    Techniques: Irradiation

    Comparison of kinase activations stimulated by fragments generated by Co-60 γ-rays and 0.75 MeV fission-neutron irradiation generated short DNA fragments. Recombinant p53 protein was incubated with DNA-PK in the presence of γ- 32 P-ATP and

    Journal: Journal of radiation research

    Article Title: Radiation-generated short DNA fragments may perturb non-homologous end-joining and induce genomic instability

    doi:

    Figure Lengend Snippet: Comparison of kinase activations stimulated by fragments generated by Co-60 γ-rays and 0.75 MeV fission-neutron irradiation generated short DNA fragments. Recombinant p53 protein was incubated with DNA-PK in the presence of γ- 32 P-ATP and

    Article Snippet: Genomic short DNA (20-400 bp) fragments generated by γ-ray or neutrons were introduced to MCF-10A cells by using lipofectin according to the manufacture's instructions (Invitrogen).

    Techniques: Generated, Irradiation, Recombinant, Incubation

    Identification of putative promoters in phi14:2 genome. a , Schematic of the phi14:2 genome (see the legend of Fig. 2a for details) with putative promoters marked by black arrows. b , Primer extension and sequencing reactions for eleven putative promoters (Supplementary Table 4). Major primer extension products are marked with black asterisks. c , Sequences flanking the primer extension endpoints are shown; nucleotides, corresponding to primer extension endpoints are colored red. Conserved nucleotides of putative middle promoters are shown in violet. d , Left panel: In vitro transcription of PCR-fragments containing the T7 A1 promoter and predicted phi14:2 P070 and P075 promoters by E. coli RNAP; Right panel: Primer extension reactions of RNA synthesized in vitro by E. coli RNAP from PCR-fragments containing phi14:2 P070 and P075 promoters.

    Journal: bioRxiv

    Article Title: Structure and function of virion RNA polymerase of crAss-like phage

    doi: 10.1101/2020.03.07.982082

    Figure Lengend Snippet: Identification of putative promoters in phi14:2 genome. a , Schematic of the phi14:2 genome (see the legend of Fig. 2a for details) with putative promoters marked by black arrows. b , Primer extension and sequencing reactions for eleven putative promoters (Supplementary Table 4). Major primer extension products are marked with black asterisks. c , Sequences flanking the primer extension endpoints are shown; nucleotides, corresponding to primer extension endpoints are colored red. Conserved nucleotides of putative middle promoters are shown in violet. d , Left panel: In vitro transcription of PCR-fragments containing the T7 A1 promoter and predicted phi14:2 P070 and P075 promoters by E. coli RNAP; Right panel: Primer extension reactions of RNA synthesized in vitro by E. coli RNAP from PCR-fragments containing phi14:2 P070 and P075 promoters.

    Article Snippet: Sequencing reactions were performed with the same primers as the ones used for the primer extension reactions and with PCR fragments (amplified from phi14:2 genomic DNA) using the USB Thermo Sequenase Cycle Sequencing Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.

    Techniques: Sequencing, In Vitro, Polymerase Chain Reaction, Synthesized

    Global analysis of phi14:2 transcription during phi14:2 infection. a , Schematics of the phi14:2 genome 3 . ORFs are marked as arrows and numbered according to the study by Yutin et al 2 (Supplementary Table 1). Intergenic regions larger than 50 base pairs are shown as grey rectangles. Replicative, gene expression, and capsid gene modules are marked by green, violet, and blue dashed frames, correspondingly 2 . Early, middle, and late genes are colored green, purple, and blue, correspondingly. Heat maps indicating the temporal pattern of phi14:2 transcripts and relative abundance of phi14:2 transcripts are shown below the genome. In the top heat map, the transcript abundance for each gene or intergenic region longer than 50 base pairs is normalized to the maximum transcript abundance for this particular gene/intergenic region; In the bottom heat map, the same quantities were normalized to the absolute maximum that corresponded to the abundance of the late gene g091 (major capsid protein) at 190 min post infection. b , Time courses of accumulation of individual phi14:2 transcripts divided into three temporal classes during infection; the y axis shows abundance of individual genes transcripts normalized to the maximal value for this gene obtained in Rif-libraries. c , Transcription by gp66 of denatured phi14:2 DNA and by C. baltica RNAP of a PCR-fragment containing the T7 A1 promoter in the absence and in the presence of rifampicin. d , Time courses of accumulation of early, middle, and late phi14:2 transcripts during infection in the presence of rifampicin; the y axis shows abundance of individual genes transcripts in Rif+ libraries normalized to maximal value for this gene obtained in Rif-libraries. e , WebLogos of phi14:2 middle promoters located upstream of middle genes g070, g075, g108, and g110 (top panel) and cumulative consensus of 126 crAss-like phage middle/late promoters (bottom panel, Supplementary file 1).

    Journal: bioRxiv

    Article Title: Structure and function of virion RNA polymerase of crAss-like phage

    doi: 10.1101/2020.03.07.982082

    Figure Lengend Snippet: Global analysis of phi14:2 transcription during phi14:2 infection. a , Schematics of the phi14:2 genome 3 . ORFs are marked as arrows and numbered according to the study by Yutin et al 2 (Supplementary Table 1). Intergenic regions larger than 50 base pairs are shown as grey rectangles. Replicative, gene expression, and capsid gene modules are marked by green, violet, and blue dashed frames, correspondingly 2 . Early, middle, and late genes are colored green, purple, and blue, correspondingly. Heat maps indicating the temporal pattern of phi14:2 transcripts and relative abundance of phi14:2 transcripts are shown below the genome. In the top heat map, the transcript abundance for each gene or intergenic region longer than 50 base pairs is normalized to the maximum transcript abundance for this particular gene/intergenic region; In the bottom heat map, the same quantities were normalized to the absolute maximum that corresponded to the abundance of the late gene g091 (major capsid protein) at 190 min post infection. b , Time courses of accumulation of individual phi14:2 transcripts divided into three temporal classes during infection; the y axis shows abundance of individual genes transcripts normalized to the maximal value for this gene obtained in Rif-libraries. c , Transcription by gp66 of denatured phi14:2 DNA and by C. baltica RNAP of a PCR-fragment containing the T7 A1 promoter in the absence and in the presence of rifampicin. d , Time courses of accumulation of early, middle, and late phi14:2 transcripts during infection in the presence of rifampicin; the y axis shows abundance of individual genes transcripts in Rif+ libraries normalized to maximal value for this gene obtained in Rif-libraries. e , WebLogos of phi14:2 middle promoters located upstream of middle genes g070, g075, g108, and g110 (top panel) and cumulative consensus of 126 crAss-like phage middle/late promoters (bottom panel, Supplementary file 1).

    Article Snippet: Sequencing reactions were performed with the same primers as the ones used for the primer extension reactions and with PCR fragments (amplified from phi14:2 genomic DNA) using the USB Thermo Sequenase Cycle Sequencing Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.

    Techniques: Infection, Expressing, Polymerase Chain Reaction

    Multiple sequence alignments of cDNA and genomic DNA amplicons amplified from 10 low and high/very high seed weight homozygous RIL mapping individuals, parental genotypes (ICC 4958 and ICC 17163), and 12 contrasting germplasm lines using the two seed weight-regulating differentially expressed CNMS marker-associated LOB-domain proten- (A) and KANADI protein-encoding (B) genes validated the presence of microsatellite repeat motifs. The presence of variable CNMS repeat units, such as (GA) n and (CAA) n , in the signal sequence-binding sites of the GAGA8HVBKN3 and RAV1AAT regulatory elements of these two genes, respectively, which differentiated all of the low seed weight germplasm lines, parents, and homozygous mapping individuals (amplifying 158bp and 150bp alleles) from the high/very high seed weight germplasm lines, parents, and homozygous RILs (160/162bp and 156bp alleles) was evident. HSL, homozygous lines. (This figure is available in colour at JXB online.)

    Journal: Journal of Experimental Botany

    Article Title: Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea

    doi: 10.1093/jxb/eru478

    Figure Lengend Snippet: Multiple sequence alignments of cDNA and genomic DNA amplicons amplified from 10 low and high/very high seed weight homozygous RIL mapping individuals, parental genotypes (ICC 4958 and ICC 17163), and 12 contrasting germplasm lines using the two seed weight-regulating differentially expressed CNMS marker-associated LOB-domain proten- (A) and KANADI protein-encoding (B) genes validated the presence of microsatellite repeat motifs. The presence of variable CNMS repeat units, such as (GA) n and (CAA) n , in the signal sequence-binding sites of the GAGA8HVBKN3 and RAV1AAT regulatory elements of these two genes, respectively, which differentiated all of the low seed weight germplasm lines, parents, and homozygous mapping individuals (amplifying 158bp and 150bp alleles) from the high/very high seed weight germplasm lines, parents, and homozygous RILs (160/162bp and 156bp alleles) was evident. HSL, homozygous lines. (This figure is available in colour at JXB online.)

    Article Snippet: For this, the cDNA and genomic DNA fragments amplifying the total coding and non-coding 5ʹ upstream sequence components (1000bp) of the differentially expressed genes in ICCX-810800, ICC 4958, and ICC 20268 were purified, cloned, and sequenced in both the forward and reverse directions twice on a capillary-based Automated DNA Sequencer (Applied Biosystems, ABI 3730xl DNA Analyzer, Vernon Hills, IL, USA).

    Techniques: Sequencing, Amplification, Immunocytochemistry, Marker, Cellular Antioxidant Activity Assay, Binding Assay

    Characterization of SMA haplotypes. (A) To characterize the extent of SMN1 deletions, we performed PCR on loci that mapped to multiple sites in the region. By selecting amplicons which exhibited sequence changes between loci, we were able to assess the presence or absence of each locus after PCR amplification and Sanger sequencing. Green blocks represent loci that were present, and red blocks denote deleted loci. The samples (i.e. haplotype combinations) are listed on the left side of the figure. (B) Competitive PCR was used to calculate SMN2 copy number in our patient cohort. Samples were subjected to multiplex PCR with limiting deoxynucleotide triphosphates and the resulting amplicons were size-fractionated on an ABI 3130 Genetic Analyzer. Samples with greater SMN2 copy number demonstrated increased generation of SMN2 -specific product versus an internal control locus (albumin gene, ALB ). (C) The area under the curve for each amplicon, as provided by the Sequencing Analysis software, was used to calculate the ratio of SMN2 -specific product to ALB product. For SMN2 copy number from 1–4, three separate samples were PCR amplified and analyzed, and the SMN2/ALB ratios were highly correlated with SMN2 copy number.

    Journal: PLoS ONE

    Article Title: Spinal muscular atrophy within Amish and Mennonite populations: Ancestral haplotypes and natural history

    doi: 10.1371/journal.pone.0202104

    Figure Lengend Snippet: Characterization of SMA haplotypes. (A) To characterize the extent of SMN1 deletions, we performed PCR on loci that mapped to multiple sites in the region. By selecting amplicons which exhibited sequence changes between loci, we were able to assess the presence or absence of each locus after PCR amplification and Sanger sequencing. Green blocks represent loci that were present, and red blocks denote deleted loci. The samples (i.e. haplotype combinations) are listed on the left side of the figure. (B) Competitive PCR was used to calculate SMN2 copy number in our patient cohort. Samples were subjected to multiplex PCR with limiting deoxynucleotide triphosphates and the resulting amplicons were size-fractionated on an ABI 3130 Genetic Analyzer. Samples with greater SMN2 copy number demonstrated increased generation of SMN2 -specific product versus an internal control locus (albumin gene, ALB ). (C) The area under the curve for each amplicon, as provided by the Sequencing Analysis software, was used to calculate the ratio of SMN2 -specific product to ALB product. For SMN2 copy number from 1–4, three separate samples were PCR amplified and analyzed, and the SMN2/ALB ratios were highly correlated with SMN2 copy number.

    Article Snippet: Extension products were size-fractionated on an ABI 3130 Genetic Analyzer and analyzed using Sequencing Analysis software (ThermoFisher Scientific, Waltham, MA).

    Techniques: Polymerase Chain Reaction, Sequencing, Amplification, Multiplex Assay, Software