pooled genomic dna Covaris Search Results


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  • 95
    Qiagen qiaamp dna micro gdna kit
    Qiaamp Dna Micro Gdna Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 95/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Zymo Research genomic dna clean and concentrator kit
    Genomic Dna Clean And Concentrator Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 95/100, based on 191 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris gdna
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Gdna, supplied by Covaris, used in various techniques. Bioz Stars score: 96/100, based on 1472 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s220
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S220, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 1788 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s2 system
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S2 System, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 742 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris e220 covaris ultrasonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    E220 Covaris Ultrasonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 90/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s220 ultrasonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S220 Ultrasonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 90/100, based on 541 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris m220
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris M220, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 1090 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s2
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S2, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 2269 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris ultrasonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris Ultrasonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 460 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris tube
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris Tube, supplied by Covaris, used in various techniques. Bioz Stars score: 92/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris sonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 1536 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris le220
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris Le220, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 470 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris afa
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris Afa, supplied by Covaris, used in various techniques. Bioz Stars score: 94/100, based on 133 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris e220
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris E220, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 792 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s220 system
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S220 System, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 288 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s2 sonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S2 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 1282 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s e210
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S E210, supplied by Covaris, used in various techniques. Bioz Stars score: 91/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris model s2
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris Model S2, supplied by Covaris, used in various techniques. Bioz Stars score: 93/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris m220 system
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris M220 System, supplied by Covaris, used in various techniques. Bioz Stars score: 89/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s220 sonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris S220 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 694 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris e200 instrument
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris E200 Instrument, supplied by Covaris, used in various techniques. Bioz Stars score: 88/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris m220 sonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris M220 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 204 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris sonication
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris Sonication, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 304 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris e220 sonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris E220 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 366 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris e220dna sonicator
    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 <t>DNA</t> (pooled D. <t>simulans</t> 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).
    Covaris E220dna Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 79/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Kapa Biosystems genomic dna
    Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK ). No genomic aberrations were found at the transcription initiation site of ALK ATI shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALK ATI is probably not caused by alterations of the <t>DNA</t> nucleotide sequence. b , c , Circos plots of the whole-genome sequencing data of MM-15 ( b ) and <t>ATC-28</t> ( c the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.
    Genomic Dna, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 95/100, based on 625 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris s2 device
    Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK ). No genomic aberrations were found at the transcription initiation site of ALK ATI shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALK ATI is probably not caused by alterations of the <t>DNA</t> nucleotide sequence. b , c , Circos plots of the whole-genome sequencing data of MM-15 ( b ) and <t>ATC-28</t> ( c the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.
    Covaris S2 Device, supplied by Covaris, used in various techniques. Bioz Stars score: 97/100, based on 344 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris covaris ngs method
    Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK ). No genomic aberrations were found at the transcription initiation site of ALK ATI shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALK ATI is probably not caused by alterations of the <t>DNA</t> nucleotide sequence. b , c , Circos plots of the whole-genome sequencing data of MM-15 ( b ) and <t>ATC-28</t> ( c the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.
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    Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK ). No genomic aberrations were found at the transcription initiation site of ALK ATI shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALK ATI is probably not caused by alterations of the <t>DNA</t> nucleotide sequence. b , c , Circos plots of the whole-genome sequencing data of MM-15 ( b ) and <t>ATC-28</t> ( c the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.
    Covaris Sonication System, supplied by Covaris, used in various techniques. Bioz Stars score: 95/100, based on 139 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK ). No genomic aberrations were found at the transcription initiation site of ALK ATI shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALK ATI is probably not caused by alterations of the <t>DNA</t> nucleotide sequence. b , c , Circos plots of the whole-genome sequencing data of MM-15 ( b ) and <t>ATC-28</t> ( c the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.
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    Image Search Results


    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).

    Journal: G3: Genes|Genomes|Genetics

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

    doi: 10.1534/g3.116.034488

    Figure Lengend 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).

    Article Snippet: We used two libraries with different read length and insert size prepared from the same genomic DNA (library 1: 2 × 76 bp paired ends, median insert size = 232 bp; library 2: 2 × 120 bp paired ends, median insert size = 396; both prepared from pooled D. simulans flies; see Materials and Methods ), trimmed low quality regions from the 3′-ends of reads, and compared allele frequency differences between the samples using F ST .

    Techniques: 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).

    Journal: G3: Genes|Genomes|Genetics

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

    doi: 10.1534/g3.116.034488

    Figure Lengend 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).

    Article Snippet: We used two libraries with different read length and insert size prepared from the same genomic DNA (library 1: 2 × 76 bp paired ends, median insert size = 232 bp; library 2: 2 × 120 bp paired ends, median insert size = 396; both prepared from pooled D. simulans flies; see Materials and Methods ), trimmed low quality regions from the 3′-ends of reads, and compared allele frequency differences between the samples using F ST .

    Techniques: Sequencing

    Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK ). No genomic aberrations were found at the transcription initiation site of ALK ATI shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALK ATI is probably not caused by alterations of the DNA nucleotide sequence. b , c , Circos plots of the whole-genome sequencing data of MM-15 ( b ) and ATC-28 ( c the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.

    Journal: Nature

    Article Title: Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

    doi: 10.1038/nature15258

    Figure Lengend Snippet: Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK ). No genomic aberrations were found at the transcription initiation site of ALK ATI shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALK ATI is probably not caused by alterations of the DNA nucleotide sequence. b , c , Circos plots of the whole-genome sequencing data of MM-15 ( b ) and ATC-28 ( c the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.

    Article Snippet: After fragmentation (E220, Covaris) of 3 μg genomic DNA of each sample (MM-15, ATC-28, H3122, and SKMEL-28), libraries were prepared with the KAPA Hyper Prep Kit (Kapa Biosystems) without PCR amplification to preserve the methylation status.

    Techniques: Sequencing, Expressing

    Alternative transcription initiation (ATI) results in a novel ALK transcript a , Distribution of RNA-seq reads of ALK variant transcripts: ALK ATI RNA-seq reads align to both ALK intron 19 and exons 20–29; full-length, wild-type ALK ( ALK WT ) RNA-seq reads align to all ALK exons, but not to the introns; translocated ALK RNA-seq reads align only to ALK exons 20–29. b , Mapping of the ATI sites of ALK ATI to a 25 bp region in ALK intron 19 (hg19 ch2:29,446,768–29,446,744; blue shaded area). c , ChIP-seq profile of H3K4me3 at the ATI site. d , Quantitative mRNA profiling of different ALK variants using Nanostring nCounter: 2 wild-type ALK -expressing neuroblastoma cell lines (SK-N-BE2 and SK-N-DZ), 2 EML4–ALK -expressing lung cancer cell lines (H3122 and H2228), 9 ALK ATI -expressing tumours (8 melanomas (MM) and 1 anaplastic thyroid carcinoma, ATC-28). e , Similar SNV frequencies in DNA-seq, RNA-seq, and ChIP-seq (H3K4me3) data indicate that ALK ATI is biallelically expressed.

    Journal: Nature

    Article Title: Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

    doi: 10.1038/nature15258

    Figure Lengend Snippet: Alternative transcription initiation (ATI) results in a novel ALK transcript a , Distribution of RNA-seq reads of ALK variant transcripts: ALK ATI RNA-seq reads align to both ALK intron 19 and exons 20–29; full-length, wild-type ALK ( ALK WT ) RNA-seq reads align to all ALK exons, but not to the introns; translocated ALK RNA-seq reads align only to ALK exons 20–29. b , Mapping of the ATI sites of ALK ATI to a 25 bp region in ALK intron 19 (hg19 ch2:29,446,768–29,446,744; blue shaded area). c , ChIP-seq profile of H3K4me3 at the ATI site. d , Quantitative mRNA profiling of different ALK variants using Nanostring nCounter: 2 wild-type ALK -expressing neuroblastoma cell lines (SK-N-BE2 and SK-N-DZ), 2 EML4–ALK -expressing lung cancer cell lines (H3122 and H2228), 9 ALK ATI -expressing tumours (8 melanomas (MM) and 1 anaplastic thyroid carcinoma, ATC-28). e , Similar SNV frequencies in DNA-seq, RNA-seq, and ChIP-seq (H3K4me3) data indicate that ALK ATI is biallelically expressed.

    Article Snippet: After fragmentation (E220, Covaris) of 3 μg genomic DNA of each sample (MM-15, ATC-28, H3122, and SKMEL-28), libraries were prepared with the KAPA Hyper Prep Kit (Kapa Biosystems) without PCR amplification to preserve the methylation status.

    Techniques: RNA Sequencing Assay, Variant Assay, Chromatin Immunoprecipitation, Expressing, DNA Sequencing