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
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Average 93 stars, based on 642 article reviews
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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
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
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
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
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
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
Article Title: Progranulin deficiency causes impairment of autophagy and TDP-43 accumulation
Article Snippet: .. Generated cDNA was sheared using
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
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
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
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
Article Title: PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies
Article Snippet: The two best known are the
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