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ultra-deep pyrosequencing data  (Pyrosequencing Inc)

 
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    Pyrosequencing Inc ultra-deep pyrosequencing data
    Ultra Deep Pyrosequencing Data, supplied by Pyrosequencing Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pyrosequencing+data/ultra+deep+pyrosequencing/pm38160480-416-13-16
    Average 90 stars, based on 1 article reviews
    ultra-deep pyrosequencing data - by Bioz Stars, 2026-09
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    Comparison:

    Article Title: Dysbiotic microbes and how to find them: a review of microbiome profiling in prostate cancer
    Article Snippet: Miyake et al., 2019 [ ] , Comparison of specific microbial taxa between prostate adenocarcinoma and BPH tissue samples from 45 RP and 33 TURP (BPH) patients , Formalin-fixed paraffin-embedded , 45 malignant and 33 BPH (n=78) , PCR screening , Increased rates of Mycoplasma genitalium was associated with Pca. , Mann-Whitney U test, P < 0.05 , Limited number of species tested.. .. Cavarretta et al., 2017 [ ] , Comparison of microbiome between tumoral, peri-tumoral, and non-tumoral tissue samples from 16 RP patients , Formalin-fixed paraffin-embedded , 16 tumoral, 16 peri-tumoral and 16 non-tumoral (n=48) , Ultradeep pyrosequencing , Actinobacteria, Firmicutes and Proteobacteria are the most abundant taxa in the prostate. Significantly increased abundances of Staphylococcus and decreased abundances of Streptococcus in tumoral + peri-tumoral tissue as compared to non-tumoral tissue samples. , Wilcoxon rank-sum test, P < 0.05 , Lack of negative control.. .. Yow et al., 2017 [ ] , Comparison of microbiome between benign (AN) and malignant tumor tissue samples from 10 RP patients , Fresh frozen tissue , 10 malignant and 10 benign (n=20) , 16s rRNA amplicon sequencing and total RNA sequencing , Enterobacteriaceae, Escherichia and Propionibacterium acnes identified as most common in both malignant and benign samples. Endogenous retroviruses could be detected in both malignant and benign samples. , n/a , Propionibacterium is a known sequencing contaminant..

    Formalin-fixed Paraffin-Embedded:

    Article Title: Dysbiotic microbes and how to find them: a review of microbiome profiling in prostate cancer
    Article Snippet: Miyake et al., 2019 [ ] , Comparison of specific microbial taxa between prostate adenocarcinoma and BPH tissue samples from 45 RP and 33 TURP (BPH) patients , Formalin-fixed paraffin-embedded , 45 malignant and 33 BPH (n=78) , PCR screening , Increased rates of Mycoplasma genitalium was associated with Pca. , Mann-Whitney U test, P < 0.05 , Limited number of species tested.. .. Cavarretta et al., 2017 [ ] , Comparison of microbiome between tumoral, peri-tumoral, and non-tumoral tissue samples from 16 RP patients , Formalin-fixed paraffin-embedded , 16 tumoral, 16 peri-tumoral and 16 non-tumoral (n=48) , Ultradeep pyrosequencing , Actinobacteria, Firmicutes and Proteobacteria are the most abundant taxa in the prostate. Significantly increased abundances of Staphylococcus and decreased abundances of Streptococcus in tumoral + peri-tumoral tissue as compared to non-tumoral tissue samples. , Wilcoxon rank-sum test, P < 0.05 , Lack of negative control.. .. Yow et al., 2017 [ ] , Comparison of microbiome between benign (AN) and malignant tumor tissue samples from 10 RP patients , Fresh frozen tissue , 10 malignant and 10 benign (n=20) , 16s rRNA amplicon sequencing and total RNA sequencing , Enterobacteriaceae, Escherichia and Propionibacterium acnes identified as most common in both malignant and benign samples. Endogenous retroviruses could be detected in both malignant and benign samples. , n/a , Propionibacterium is a known sequencing contaminant..

    Negative Control:

    Article Title: Dysbiotic microbes and how to find them: a review of microbiome profiling in prostate cancer
    Article Snippet: Miyake et al., 2019 [ ] , Comparison of specific microbial taxa between prostate adenocarcinoma and BPH tissue samples from 45 RP and 33 TURP (BPH) patients , Formalin-fixed paraffin-embedded , 45 malignant and 33 BPH (n=78) , PCR screening , Increased rates of Mycoplasma genitalium was associated with Pca. , Mann-Whitney U test, P < 0.05 , Limited number of species tested.. .. Cavarretta et al., 2017 [ ] , Comparison of microbiome between tumoral, peri-tumoral, and non-tumoral tissue samples from 16 RP patients , Formalin-fixed paraffin-embedded , 16 tumoral, 16 peri-tumoral and 16 non-tumoral (n=48) , Ultradeep pyrosequencing , Actinobacteria, Firmicutes and Proteobacteria are the most abundant taxa in the prostate. Significantly increased abundances of Staphylococcus and decreased abundances of Streptococcus in tumoral + peri-tumoral tissue as compared to non-tumoral tissue samples. , Wilcoxon rank-sum test, P < 0.05 , Lack of negative control.. .. Yow et al., 2017 [ ] , Comparison of microbiome between benign (AN) and malignant tumor tissue samples from 10 RP patients , Fresh frozen tissue , 10 malignant and 10 benign (n=20) , 16s rRNA amplicon sequencing and total RNA sequencing , Enterobacteriaceae, Escherichia and Propionibacterium acnes identified as most common in both malignant and benign samples. Endogenous retroviruses could be detected in both malignant and benign samples. , n/a , Propionibacterium is a known sequencing contaminant..

    other:

    Article Title: Intact proviruses are enriched in the colon and associated with PD-1 + TIGIT - mucosal CD4 + T cells of people with HIV-1 on antiretroviral therapy.
    Article Snippet: 35 Jeanne N, Saliou A, Carcenac R, et al. Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.

    Article Title: Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis.
    Article Snippet: Even though the diversity of the sequences could support the inference ransmission in three lawsuits Using Ultra-Deep pyrosequencing and tion, https://doi.org/10.1016/j.jmii.2019.12.002 of the prosecutor, the combined used of a molecular clock approach may have provided further information to demonstrate a more accurate transmission event and timing.42 43 Moreover, the main difficulty in the application of the phylogenetic method for forensic purposes is still the validity of expert testimony to convince the judge and prosecutor.

    Article Title: Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis.
    Article Snippet: Phylogenetic tree analysis using gag nucleotide sequences from Ultra-Deep Pyrosequencing of lawsuit 2.

    Article Title: Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis.
    Article Snippet: Otherwise, the gag Bayesian tree result with local ransmission in three lawsuits Using Ultra-Deep pyrosequencing and tion, https://doi.org/10.1016/j.jmii.2019.12.002 controls showed that the sequences from both individuals located on same phylogenetic branch (Bayesian posterior probability values of 1), and all the sequences from A10003 formed a monophyletic cluster nested in A10004’s Please cite this article as: Li W-Y et al., Source identification of HIV-1 t phylogenetic analysis, Journal of Microbiology, Immunology and Infect sequences that presented a PM pattern (Fig. 4).

    Multiplex Assay:

    Article Title: Cytokine profile and viral diversity in the early seronegative stage of community-acquired hepatitis C virus (HCV) infection.
    Article Snippet: .. Hypervariable region 1 was analyzed by ultradeep pyrosequencing and cytokines in serum were quantified by Luminex (R&D Systems) multiplex immunoassay. ..



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    RADDIM creates random duplications or deletions at one random position within a circular DNA molecule. ( A ) Illustration of the RADDIM workflow when starting from a plasmid template. Illustration created with BioRender.com . ( B ) An ExoChase-treated pUC19 plasmid (Fig. ) containing a CcdB toxin gene was nicked on the forward DNA-strand by the site-specific nickase Nt.BbvCI. The resulting double-nicked plasmids were incubated with Bst DNAP, with or without either the 5′–3′ single-strand-specific RecJ exonuclease, or the 3′–5′ single-strand-specific Thermolabile Exonuclease I, to determine if single-strand exonucleases could remove unwanted DNA-amplifications during a convergent nick-translation reaction. ( C ) Characterization of the DNA-ends that were created by a convergent nick-translation reaction using Bst DNAP and either RecJ or Thermolabile Exo I (Fig. ). ConNickTra linearized plasmids were purified and T7 DNAP was used to repair all DNA-ends. Next, T4 DNA ligase was used to re-circularize the linear plasmids, which were transformed into CcdB-sensitive E. coli cells. This selected for plasmids with a mutation in the ccdB toxin gene. The ccdB gene of 40 successfully sequenced plasmids from the RecJ library ( n = 40), and 39 successfully sequenced plasmids from the Thermolabile Exo I library ( n = 39) were sequenced by single-colony Sanger sequencing. ( D ) A synthetic 196 bp dsDNA fragment was incubated together with Bst DNAP alone, and/or Thermolabile Exo I, for 3 h with or without 1 mM MnCl 2 , to evaluate if manganese could reprogram the Bst DNAP and/or ExoI to degrade the ends of linear DNA molecules. ( E ) A pUC19 plasmid containing a CcdB toxin gene was randomly linearized by a ConNickTra reaction using Bst DNAP and ExoI, followed by an addition of 1 mM MnCl 2 for 10–30 min. After a T7 DNAP-mediated DNA end-repair, and a T4 DNA ligase-mediated re-circularization, plasmids were transformed into CcdB-sensitive E. coli cells. ( F ) The ccdB gene of 25 successfully sequenced plasmids from the 10 min library ( n = 25), 21 plasmids from the 20 min library ( n = 21), and 22 successfully sequenced plasmids from the 30 min library ( n = 22) were analyzed by single-colony Sanger sequencing.

    Journal: Nucleic Acids Research

    Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

    doi: 10.1093/nar/gkag236

    Figure Lengend Snippet: RADDIM creates random duplications or deletions at one random position within a circular DNA molecule. ( A ) Illustration of the RADDIM workflow when starting from a plasmid template. Illustration created with BioRender.com . ( B ) An ExoChase-treated pUC19 plasmid (Fig. ) containing a CcdB toxin gene was nicked on the forward DNA-strand by the site-specific nickase Nt.BbvCI. The resulting double-nicked plasmids were incubated with Bst DNAP, with or without either the 5′–3′ single-strand-specific RecJ exonuclease, or the 3′–5′ single-strand-specific Thermolabile Exonuclease I, to determine if single-strand exonucleases could remove unwanted DNA-amplifications during a convergent nick-translation reaction. ( C ) Characterization of the DNA-ends that were created by a convergent nick-translation reaction using Bst DNAP and either RecJ or Thermolabile Exo I (Fig. ). ConNickTra linearized plasmids were purified and T7 DNAP was used to repair all DNA-ends. Next, T4 DNA ligase was used to re-circularize the linear plasmids, which were transformed into CcdB-sensitive E. coli cells. This selected for plasmids with a mutation in the ccdB toxin gene. The ccdB gene of 40 successfully sequenced plasmids from the RecJ library ( n = 40), and 39 successfully sequenced plasmids from the Thermolabile Exo I library ( n = 39) were sequenced by single-colony Sanger sequencing. ( D ) A synthetic 196 bp dsDNA fragment was incubated together with Bst DNAP alone, and/or Thermolabile Exo I, for 3 h with or without 1 mM MnCl 2 , to evaluate if manganese could reprogram the Bst DNAP and/or ExoI to degrade the ends of linear DNA molecules. ( E ) A pUC19 plasmid containing a CcdB toxin gene was randomly linearized by a ConNickTra reaction using Bst DNAP and ExoI, followed by an addition of 1 mM MnCl 2 for 10–30 min. After a T7 DNAP-mediated DNA end-repair, and a T4 DNA ligase-mediated re-circularization, plasmids were transformed into CcdB-sensitive E. coli cells. ( F ) The ccdB gene of 25 successfully sequenced plasmids from the 10 min library ( n = 25), 21 plasmids from the 20 min library ( n = 21), and 22 successfully sequenced plasmids from the 30 min library ( n = 22) were analyzed by single-colony Sanger sequencing.

    Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

    Techniques: Plasmid Preparation, Incubation, Nick Translation, Purification, Transformation Assay, Mutagenesis, Sequencing

    RADDIM allows for in-frame and multi-residue InDels enabling functional protein structure modifications. ( A ) Illustration of an alternative RADDIM workflow to insert random DNA sequences into a RADDIM library by ligating a random DNA sequence oligo library to ConNickTra linearized plasmids, followed by a T7 DNAP-mediated DNA-end-repair/fill-in. Illustration created with BioRender.com . ( B ) Representative β-lactamase compensatory mutations able to restore phenotypic ampicillin resistance of the enzymatically inactivated (A40P and R41W) TEM-1 protein, superimposed onto the wild-type TEM-1 protein structure (PDB: 1ZG4). Red spheres = original inactivating mutations (A40P and R41W), Green spheres = compensatory AA substitutions. Purple marking = site of multi-residue compensatory deletion. Brown marking = site of multi-residue compensatory insertions.

    Journal: Nucleic Acids Research

    Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

    doi: 10.1093/nar/gkag236

    Figure Lengend Snippet: RADDIM allows for in-frame and multi-residue InDels enabling functional protein structure modifications. ( A ) Illustration of an alternative RADDIM workflow to insert random DNA sequences into a RADDIM library by ligating a random DNA sequence oligo library to ConNickTra linearized plasmids, followed by a T7 DNAP-mediated DNA-end-repair/fill-in. Illustration created with BioRender.com . ( B ) Representative β-lactamase compensatory mutations able to restore phenotypic ampicillin resistance of the enzymatically inactivated (A40P and R41W) TEM-1 protein, superimposed onto the wild-type TEM-1 protein structure (PDB: 1ZG4). Red spheres = original inactivating mutations (A40P and R41W), Green spheres = compensatory AA substitutions. Purple marking = site of multi-residue compensatory deletion. Brown marking = site of multi-residue compensatory insertions.

    Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

    Techniques: Residue, Functional Assay, Sequencing

    Deep sequencing confirms the diversity of RADDIM-generated InDel libraries. ( A ) Size distribution of insertions and deletions across a RADDIM plasmid library and the location of all variants (insertions and deletions) that are 1 nt and >1 nt in length. InDels are shown by their start position in the 5′–3′ direction in the plasmid sequence. Positive values represent insertions and negative values represent deletions. CAT = chloramphenicol acetyltransferase, tCYC1 = transcriptional terminator of iso-1-cytochrome c from S. cerevisiae , ori = pUC19 origin-of-replication, BLA* = inactivated (A40P and R41W) β-lactamase (TEM-1), CcdB = bacterial DNA gyrase toxin, CcdA* = inactivated cognate immunity protein of CcdB. ( B ) Illustration of the plasmid linearization mechanisms attained by combining the ExoChase and ConNickTra methods, enabling random and singular double-stranded DNA-breaks to be enriched within only one half of a plasmid molecule, down-stream of the site-specific DNA-nick. Illustration created with BioRender.com . ( C ) Quantification of all identified deletions ranging from 1 to 30 nt in length. ( D ) Quantification of all identified insertions ranging from 1 to 30 nt in length. ( E ) The number of identified mismatches for all insertions ranging from 2 to 30 nt in length.

    Journal: Nucleic Acids Research

    Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

    doi: 10.1093/nar/gkag236

    Figure Lengend Snippet: Deep sequencing confirms the diversity of RADDIM-generated InDel libraries. ( A ) Size distribution of insertions and deletions across a RADDIM plasmid library and the location of all variants (insertions and deletions) that are 1 nt and >1 nt in length. InDels are shown by their start position in the 5′–3′ direction in the plasmid sequence. Positive values represent insertions and negative values represent deletions. CAT = chloramphenicol acetyltransferase, tCYC1 = transcriptional terminator of iso-1-cytochrome c from S. cerevisiae , ori = pUC19 origin-of-replication, BLA* = inactivated (A40P and R41W) β-lactamase (TEM-1), CcdB = bacterial DNA gyrase toxin, CcdA* = inactivated cognate immunity protein of CcdB. ( B ) Illustration of the plasmid linearization mechanisms attained by combining the ExoChase and ConNickTra methods, enabling random and singular double-stranded DNA-breaks to be enriched within only one half of a plasmid molecule, down-stream of the site-specific DNA-nick. Illustration created with BioRender.com . ( C ) Quantification of all identified deletions ranging from 1 to 30 nt in length. ( D ) Quantification of all identified insertions ranging from 1 to 30 nt in length. ( E ) The number of identified mismatches for all insertions ranging from 2 to 30 nt in length.

    Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

    Techniques: Sequencing, Generated, Plasmid Preparation

    RADDIM enables a random duplication or deletion of entire regulatory DNA motifs. ( A ) Illustration of the last steps in the RADDIM workflow when starting from a linear PCR-product (Fig. ). Illustration created with BioRender.com . Relative mNeonGreen fluorescent protein expression by S. cerevisiae cells transformed with RADDIM-mutated ( B ) pACT1 ( n = 90) or ( C ) pTEF1 promoter variants ( n = 86) following a FACS of top 1% of fluorescent cells. ( D ) Relative mNeonGreen fluorescent protein expression by reconstituted pACT1 and pTEF1 promoter variants ( n = 3). Statistical significance was calculated by two-way ANOVA with ns: P > 0.05, *: P ≤ 0.05, **: P ≤ 0.005, ***: P ≤ 0.0005, and ****: P ≤ 0.0001. ( E) Relative mNeonGreen fluorescent protein expression by wild-type pACT1 and pTEF1 promoters ( n = 3). Statistical significance was calculated by unpaired t -test with ns: P > 0.05 and *: P ≤ 0.0001.

    Journal: Nucleic Acids Research

    Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

    doi: 10.1093/nar/gkag236

    Figure Lengend Snippet: RADDIM enables a random duplication or deletion of entire regulatory DNA motifs. ( A ) Illustration of the last steps in the RADDIM workflow when starting from a linear PCR-product (Fig. ). Illustration created with BioRender.com . Relative mNeonGreen fluorescent protein expression by S. cerevisiae cells transformed with RADDIM-mutated ( B ) pACT1 ( n = 90) or ( C ) pTEF1 promoter variants ( n = 86) following a FACS of top 1% of fluorescent cells. ( D ) Relative mNeonGreen fluorescent protein expression by reconstituted pACT1 and pTEF1 promoter variants ( n = 3). Statistical significance was calculated by two-way ANOVA with ns: P > 0.05, *: P ≤ 0.05, **: P ≤ 0.005, ***: P ≤ 0.0005, and ****: P ≤ 0.0001. ( E) Relative mNeonGreen fluorescent protein expression by wild-type pACT1 and pTEF1 promoters ( n = 3). Statistical significance was calculated by unpaired t -test with ns: P > 0.05 and *: P ≤ 0.0001.

    Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

    Techniques: Expressing, Transformation Assay