500 bp fragments  (Covaris)


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    Covaris 500 bp fragments
    The workflow to screen for regulatory SNPs associated with cancer risk. The genomic DNA from ten individuals was pooled and sonicated into fragments of ~ <t>500</t> bp. Regions containing 10,673 SNPs in LD with 996 GWAS-identified cancer
    500 Bp Fragments, supplied by Covaris, used in various techniques. Bioz Stars score: 93/100, based on 642 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/500 bp fragments/product/Covaris
    Average 93 stars, based on 642 article reviews
    Price from $9.99 to $1999.99
    500 bp fragments - by Bioz Stars, 2020-05
    93/100 stars

    Images

    1) Product Images from "Systematic identification of regulatory variants associated with cancer risk"

    Article Title: Systematic identification of regulatory variants associated with cancer risk

    Journal: Genome Biology

    doi: 10.1186/s13059-017-1322-z

    The workflow to screen for regulatory SNPs associated with cancer risk. The genomic DNA from ten individuals was pooled and sonicated into fragments of ~ 500 bp. Regions containing 10,673 SNPs in LD with 996 GWAS-identified cancer
    Figure Legend Snippet: The workflow to screen for regulatory SNPs associated with cancer risk. The genomic DNA from ten individuals was pooled and sonicated into fragments of ~ 500 bp. Regions containing 10,673 SNPs in LD with 996 GWAS-identified cancer

    Techniques Used: Sonication, GWAS

    2) Product Images from "Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity"

    Article Title: Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity

    Journal: Scientific Reports

    doi: 10.1038/srep21762

    Coverage plots. ( A ) Coverage of mitogenomes from 16 species of Schizophora generated by long-range PCR and shotgun sequencing. Highlighted regions indicate an overlap (green) and the 16S gap (orange) region between the two amplicons. Gaps in 16S sequence were further closed through standard PCR and Sanger sequencing. ( B ) 16 mitogenomes assembled from short reads generated by whole genome sequencing. Both strategies used short reads from MiSeq or HiSeq Illumina platforms to generate high-quality assemblies. ( C ) Coverage plot of the complete mtDNA assembled with long reads generated with SMRT sequencing technology. The scheme shows the complete mtDNA of C. megacephala (sample F03) assembled with 15,835 bp. First track shows the low GC content (23.5%). Orange bars on the second track refer to the coverage. The innermost track shows gene order in each mtDNA strand. Yellow arrows denote PCGs, green arrows show rRNA subunits and orange arrows refer to tRNAs.
    Figure Legend Snippet: Coverage plots. ( A ) Coverage of mitogenomes from 16 species of Schizophora generated by long-range PCR and shotgun sequencing. Highlighted regions indicate an overlap (green) and the 16S gap (orange) region between the two amplicons. Gaps in 16S sequence were further closed through standard PCR and Sanger sequencing. ( B ) 16 mitogenomes assembled from short reads generated by whole genome sequencing. Both strategies used short reads from MiSeq or HiSeq Illumina platforms to generate high-quality assemblies. ( C ) Coverage plot of the complete mtDNA assembled with long reads generated with SMRT sequencing technology. The scheme shows the complete mtDNA of C. megacephala (sample F03) assembled with 15,835 bp. First track shows the low GC content (23.5%). Orange bars on the second track refer to the coverage. The innermost track shows gene order in each mtDNA strand. Yellow arrows denote PCGs, green arrows show rRNA subunits and orange arrows refer to tRNAs.

    Techniques Used: Generated, Polymerase Chain Reaction, Shotgun Sequencing, Sequencing

    3) Product Images from "Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data"

    Article Title: Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data

    Journal: G3: Genes|Genomes|Genetics

    doi: 10.1534/g3.116.034488

    Comparison of allele frequency differences between real Pool-Seq data sets with different mapping algorithms. We compared allele frequencies between two paired end libraries with different read length and insert size that were prepared from the same genomic DNA (pooled D. simulans flies). We determined the lowest F ST -values in different quantiles with the most differentiated SNPs. Algorithms are sorted according to performance, with best the performing algorithm shown at the top (minimizing the F ST in the 0.001% outlier quantile). mrfast generated an invalid output file with these data (an uniform read length was reported despite these reads having varying read lengths).
    Figure Legend Snippet: Comparison of allele frequency differences between real Pool-Seq data sets with different mapping algorithms. We compared allele frequencies between two paired end libraries with different read length and insert size that were prepared from the same genomic DNA (pooled D. simulans flies). We determined the lowest F ST -values in different quantiles with the most differentiated SNPs. Algorithms are sorted according to performance, with best the performing algorithm shown at the top (minimizing the F ST in the 0.001% outlier quantile). mrfast generated an invalid output file with these data (an uniform read length was reported despite these reads having varying read lengths).

    Techniques Used: Generated

    Manhattan plots indicating the significance of allele frequency differences between Pool-Seq libraries when the same genomic DNA is sequenced. Two Illumina paired-end sequencing libraries with different read length and insert sizes were prepared from a pool of 250 D. simulans individuals. Reads were mapped to the reference genome, and the significance of differences in allele frequencies between the two libraries were computed (Fisher’s exact test). Although no significant allele frequency differences were expected, we found pronounced outlier peaks using bwa aln (A) or novoalign(g) (B) for mapping the reads. Importantly, outlier peaks found with these two alignment algorithms are at different genomic sites. Hence, intersecting the results of these two algorithms by plotting the lowest P -value obtained at each site removes the vast majority of outlier peaks (C).
    Figure Legend Snippet: Manhattan plots indicating the significance of allele frequency differences between Pool-Seq libraries when the same genomic DNA is sequenced. Two Illumina paired-end sequencing libraries with different read length and insert sizes were prepared from a pool of 250 D. simulans individuals. Reads were mapped to the reference genome, and the significance of differences in allele frequencies between the two libraries were computed (Fisher’s exact test). Although no significant allele frequency differences were expected, we found pronounced outlier peaks using bwa aln (A) or novoalign(g) (B) for mapping the reads. Importantly, outlier peaks found with these two alignment algorithms are at different genomic sites. Hence, intersecting the results of these two algorithms by plotting the lowest P -value obtained at each site removes the vast majority of outlier peaks (C).

    Techniques Used: Sequencing

    Related Articles

    Sequencing:

    Article Title: The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity.
    Article Snippet: .. For sequencing on the Illumina platform, 1 ug of genomic DNA was sheared to 400 bp using Covaris LE220 Focused-ultrasonicator (Covaris, Woburn, MA). .. End repair, A-tailing and ligation of adapters were performed on the Apollo 324 automated system, using Prep X Complete ILMN DNA Library Kit (WaferGen Biosystems, Fremont, CA).

    Generated:

    Article Title: Progranulin deficiency causes impairment of autophagy and TDP-43 accumulation
    Article Snippet: .. Generated cDNA was sheared using LE220 focused ultrasonicator (Covaris) and quantified by Qubit dsDNA BR Assay (Life Technologies). .. 1 µg sheared cDNA was taken into library generation, starting at the end repair step, using the TruSeq RNA Sample Preparation kit v2 (Illumina).

    other:

    Article Title: CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies
    Article Snippet: We sheared 400 ng of gDNA using a Covaris LE220 Ultrasonicator to an average length of 500 bp.

    Article Title: Genomic dissection of a ‘Fuji’ apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection
    Article Snippet: DNA was fragmented with a LE220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).

    Article Title: Gene correction for SCID-X1 in long-term hematopoietic stem cells
    Article Snippet: In all, 400 ng of gDNA was sheared using a Covaris LE220 Ultrasonicator to an average length of 500 bp.

    Article Title: Phylogeography of Burkholderia pseudomallei Isolates, Western Hemisphere
    Article Snippet: Genomic DNA was sheared to a mean size of 600 bp by using an LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA).

    Article Title: PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies
    Article Snippet: The two best known are the Bioruptor (manufactured by Diagenode), and LE220 Focused Ultrasonicator (manufactured by Covaris).

    Software:

    Article Title: Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment
    Article Snippet: .. Briefly, DNA samples (50 μl in a 96-well microTUBE plate) were sheared using a Covaris LE220 focused ultrasonicator with SonoLab 7.3.2.4 software (Covaris, Inc., Woburn, MA). .. The conditions used for shearing (duty factor, 15%; peak incident power, 450; treatment time, 490 s) generated DNA fragments with a peak around 150 bp as determined by the high-sensitivity DNA kit and a Bioanalyzer 2100 (Agilent Technologies).

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    Covaris cyanophage genomic dna
    Proposed role of 2-oxoglutarate (2OG) during <t>cyanophage</t> infection. A. In uninfected cyanobacteria, nitrogen limitation causes 2OG to accumulate, leading to 2OG-dependent binding of NtcA to promoters of nitrogen-stress genes, resulting in their expression. B. Phage infection draws down cellular nitrogen causing N-stress and likely leading to 2OG accumulation. Several cyanophage-encoded enzymes (in bold) suggest that increased 2OG may facilitate phage infection. First, a putative phytanoyl-CoA dioxygenase may convert 2OG to succinate, a major electron donor to respiratory electron transport in cyanobacteria ( Cooley and Vermaas, 2001 ) thus potentially generating energy for the infection process. Second, 2OG-dependent dioxygenase [2OG-Fe(II)] superfamily proteins may function in cyanophage <t>DNA</t> repair ( Weigele et al ., 2007 ). Third, cyanophage genomes have multiple NtcA promoters driving genes encoding diverse functions – possibly exploiting the host NtcA-driven N-stress response system.
    Cyanophage Genomic Dna, supplied by Covaris, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cyanophage genomic dna/product/Covaris
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    cyanophage genomic dna - by Bioz Stars, 2020-05
    85/100 stars
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    Proposed role of 2-oxoglutarate (2OG) during cyanophage infection. A. In uninfected cyanobacteria, nitrogen limitation causes 2OG to accumulate, leading to 2OG-dependent binding of NtcA to promoters of nitrogen-stress genes, resulting in their expression. B. Phage infection draws down cellular nitrogen causing N-stress and likely leading to 2OG accumulation. Several cyanophage-encoded enzymes (in bold) suggest that increased 2OG may facilitate phage infection. First, a putative phytanoyl-CoA dioxygenase may convert 2OG to succinate, a major electron donor to respiratory electron transport in cyanobacteria ( Cooley and Vermaas, 2001 ) thus potentially generating energy for the infection process. Second, 2OG-dependent dioxygenase [2OG-Fe(II)] superfamily proteins may function in cyanophage DNA repair ( Weigele et al ., 2007 ). Third, cyanophage genomes have multiple NtcA promoters driving genes encoding diverse functions – possibly exploiting the host NtcA-driven N-stress response system.

    Journal: Environmental Microbiology

    Article Title: Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

    doi: 10.1111/j.1462-2920.2010.02280.x

    Figure Lengend Snippet: Proposed role of 2-oxoglutarate (2OG) during cyanophage infection. A. In uninfected cyanobacteria, nitrogen limitation causes 2OG to accumulate, leading to 2OG-dependent binding of NtcA to promoters of nitrogen-stress genes, resulting in their expression. B. Phage infection draws down cellular nitrogen causing N-stress and likely leading to 2OG accumulation. Several cyanophage-encoded enzymes (in bold) suggest that increased 2OG may facilitate phage infection. First, a putative phytanoyl-CoA dioxygenase may convert 2OG to succinate, a major electron donor to respiratory electron transport in cyanobacteria ( Cooley and Vermaas, 2001 ) thus potentially generating energy for the infection process. Second, 2OG-dependent dioxygenase [2OG-Fe(II)] superfamily proteins may function in cyanophage DNA repair ( Weigele et al ., 2007 ). Third, cyanophage genomes have multiple NtcA promoters driving genes encoding diverse functions – possibly exploiting the host NtcA-driven N-stress response system.

    Article Snippet: Briefly, 100 µl of cyanophage genomic DNA (1 ng to 2.2 µg) was sheared using Covaris AFA technology and the following conditions: time = 240 s, duty cycle = 5, intensity = 5; cycles per burst = 200 and temperature = 3°C.

    Techniques: Infection, Binding Assay, Expressing