cdna library construction Illumina Inc Search Results


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  • 99
    Illumina Inc nextera xt library construction kit
    Nextera Xt Library Construction Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextera xt library construction kit/product/Illumina Inc
    Average 99 stars, based on 321 article reviews
    Price from $9.99 to $1999.99
    nextera xt library construction kit - by Bioz Stars, 2019-08
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    98
    Illumina Inc dna library construction
    Genome-wide base composition bias curves in <t>Illumina</t> reads from PCR-free human <t>DNA</t> libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.
    Dna Library Construction, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 98/100, based on 195 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna library construction/product/Illumina Inc
    Average 98 stars, based on 195 article reviews
    Price from $9.99 to $1999.99
    dna library construction - by Bioz Stars, 2019-08
    98/100 stars
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    80
    Illumina Inc truseq dna library construction
    Genome-wide base composition bias curves in <t>Illumina</t> reads from PCR-free human <t>DNA</t> libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.
    Truseq Dna Library Construction, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 80/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq dna library construction/product/Illumina Inc
    Average 80 stars, based on 54 article reviews
    Price from $9.99 to $1999.99
    truseq dna library construction - by Bioz Stars, 2019-08
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    99
    Illumina Inc nextera xt dna 96 kit
    Genome-wide base composition bias curves in <t>Illumina</t> reads from PCR-free human <t>DNA</t> libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.
    Nextera Xt Dna 96 Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextera xt dna 96 kit/product/Illumina Inc
    Average 99 stars, based on 29 article reviews
    Price from $9.99 to $1999.99
    nextera xt dna 96 kit - by Bioz Stars, 2019-08
    99/100 stars
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    90
    Illumina Inc rdna
    Contribution of the main phylogenetic groups classified at order level in the controls with no OPE addition (x axis) and in the OPE addition treatments (amendment with 200 ng/L final nominal concentration, y axis) to the total abundance (% total <t>16S</t> <t>rDNA,</t> left panel) and the potential activity (% total rRNA reads, right panel). The values are the average of two replicates. Error bars indicate standard deviation.
    Rdna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rdna/product/Illumina Inc
    Average 90 stars, based on 22 article reviews
    Price from $9.99 to $1999.99
    rdna - by Bioz Stars, 2019-08
    90/100 stars
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    83
    Illumina Inc 16s rdna v6
    Enrichment of A. parvulum and altered mitochondrial proteome define the severity of Crohn's disease. ( a ) Interaction network of differentially abundant OTUs; each node represents an OTU and are sized according to their number of interactions; each edge denotes a significant co-exclusion (red) or co-occurence (grey) relationship between OTUs. Nodes are coloured by their number of significant co-exclusions. ( b ) The qPCR quantification of A. parvulum in control and CD microbiota as a function of disease severity. ΔCt was calculated by subtracting average Ct values of universal <t>16S</t> <t>rDNA</t> from average Ct values of A. parvulum specific primers ( n =18 for controls, nine for mild CD and seven for moderate and severe CD). ** P
    16s Rdna V6, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 83/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/16s rdna v6/product/Illumina Inc
    Average 83 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    16s rdna v6 - by Bioz Stars, 2019-08
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    Image Search Results


    Genome-wide base composition bias curves in Illumina reads from PCR-free human DNA libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.

    Journal: Scientific Reports

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA

    doi: 10.1038/s41598-018-34079-2

    Figure Lengend Snippet: Genome-wide base composition bias curves in Illumina reads from PCR-free human DNA libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.

    Article Snippet: To further assess the utility of the immobilized enzymes method on more challenging samples, we have performed Illumina DNA library construction using human FFPE DNA with or without DNA repair as described previously .

    Techniques: Genome Wide, Polymerase Chain Reaction, Gas Chromatography, Produced, Generated, Incubation, Selection

    Effect of end repair and 3′ A-tailing at high temperature on GC-bias in Illumina reads from PCR-free human DNA libraries. ( a ) Comparison of GC-bias curves in duplicate libraries prepared by immobilized enzymes with 3′ A-tailing performed at 37 °C (IM 37 °C -1 and IM 37 °C -2, in blue) or 65 °C (IM 65 °C -1 and IM 65 °C -2, in green) revealed a dramatic effect of 3′ A-tailing at high temperature on sequence coverage of the AT-rich regions from human DNA libraries. ( b ) GC-bias curves were generated from two sets of duplicate libraries produced using the soluble enzyme mixture PKT with (PKT purify-1 and PKT purify-2) or without (PKT-1 and PKT-2) a purification step between end repair and high temperature incubation (with Taq DNA pol added to the samples following purification). Although some bias against AT-rich regions can be attributed to the end repair step, the elevated temperature contributes to the majority of the dropouts in the AT-rich regions. ( c ) Shown are the GC-bias curves from 4 sets of duplicate libraries produced by the method of soluble enzymes. Two sets of the duplicate libraries were purified after end repair with PK mixture and then treated at 37 °C with Klenow Fragment (3′-5′ exo − ) (red, Klenow 37 °C-1 and Klenow 37 °C-2) or Taq DNA pol (blue, Taq 37 °C-1 and Taq 37 °C-2). The other two duplicate sets were prepared using the high temperature treatment protocol either with (green, Taq 65 °C-1 and Taq 65 °C-2) or without (orange, PKT-1 and PKT-2) a purification step between end repair with PKT and treatment with Taq DNA pol at 65 °C for 30 min. ( d ) Comparison of library yield of the three sets described above with or without (PKT on the left) a purification step between end repair and 3′ A-tailing indicates that purification caused substantial loss of library DNA.

    Journal: Scientific Reports

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA

    doi: 10.1038/s41598-018-34079-2

    Figure Lengend Snippet: Effect of end repair and 3′ A-tailing at high temperature on GC-bias in Illumina reads from PCR-free human DNA libraries. ( a ) Comparison of GC-bias curves in duplicate libraries prepared by immobilized enzymes with 3′ A-tailing performed at 37 °C (IM 37 °C -1 and IM 37 °C -2, in blue) or 65 °C (IM 65 °C -1 and IM 65 °C -2, in green) revealed a dramatic effect of 3′ A-tailing at high temperature on sequence coverage of the AT-rich regions from human DNA libraries. ( b ) GC-bias curves were generated from two sets of duplicate libraries produced using the soluble enzyme mixture PKT with (PKT purify-1 and PKT purify-2) or without (PKT-1 and PKT-2) a purification step between end repair and high temperature incubation (with Taq DNA pol added to the samples following purification). Although some bias against AT-rich regions can be attributed to the end repair step, the elevated temperature contributes to the majority of the dropouts in the AT-rich regions. ( c ) Shown are the GC-bias curves from 4 sets of duplicate libraries produced by the method of soluble enzymes. Two sets of the duplicate libraries were purified after end repair with PK mixture and then treated at 37 °C with Klenow Fragment (3′-5′ exo − ) (red, Klenow 37 °C-1 and Klenow 37 °C-2) or Taq DNA pol (blue, Taq 37 °C-1 and Taq 37 °C-2). The other two duplicate sets were prepared using the high temperature treatment protocol either with (green, Taq 65 °C-1 and Taq 65 °C-2) or without (orange, PKT-1 and PKT-2) a purification step between end repair with PKT and treatment with Taq DNA pol at 65 °C for 30 min. ( d ) Comparison of library yield of the three sets described above with or without (PKT on the left) a purification step between end repair and 3′ A-tailing indicates that purification caused substantial loss of library DNA.

    Article Snippet: To further assess the utility of the immobilized enzymes method on more challenging samples, we have performed Illumina DNA library construction using human FFPE DNA with or without DNA repair as described previously .

    Techniques: Gas Chromatography, Polymerase Chain Reaction, Sequencing, Generated, Produced, Purification, Incubation

    Enzyme immobilization and comparison of Illumina library preparation protocols. ( a ) A schematic of covalent conjugation of SNAP-tagged enzyme fusion proteins to magnetic beads functionalized with O 6 -benzylguanine (BG) moieties that specifically react with active site cysteine residues of SNAP-tag proteins, forming a stable covalent thioether bond 15 , 16 . ( b ) Workflow for library construction using immobilized enzymes for Illumina sequencing. A typical streamlined protocol for Illumina library construction is modified by employing immobilized enzymes to catalyze end repair and 3′ A-tailing. This method utilizes SNAP-tagged T4 DNA pol and PNK covalently conjugated to BG-functionalized magnetic beads to carry out end repair of fragmented DNA at 20°C (or 37 °C) for 30 min. The enzymes are removed by magnetic separation from the DNA pool, which is subjected to 3′ A-tailing at 37 °C for 30 min using immobilized Taq DNA pol. ( c ) Streamlined protocol for Illumina amplification-free library preparation using soluble enzymes. Typically, end repair and 3′ A-tailing of fragmented DNA are catalyzed by an enzyme mixture at 20 °C for 30 min, followed by heat treatment at 65 °C for 30 min. ( d ) The workflow of Illumina TruSeq DNA PCR-free LT Library Prep Kit with a purification step. End repair is performed for 30 min at 30 °C, followed by a bead-based step for clean up and size selection. 3′ A-tailing is carried out for 30 min at 37 °C with a subsequent treatment for 5 min at 70 °C. Each library was ligated to preannealed full-length paired-end Illumina adaptors, size-selected and analyzed, and sequenced on an Illumina sequencing platform.

    Journal: Scientific Reports

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA

    doi: 10.1038/s41598-018-34079-2

    Figure Lengend Snippet: Enzyme immobilization and comparison of Illumina library preparation protocols. ( a ) A schematic of covalent conjugation of SNAP-tagged enzyme fusion proteins to magnetic beads functionalized with O 6 -benzylguanine (BG) moieties that specifically react with active site cysteine residues of SNAP-tag proteins, forming a stable covalent thioether bond 15 , 16 . ( b ) Workflow for library construction using immobilized enzymes for Illumina sequencing. A typical streamlined protocol for Illumina library construction is modified by employing immobilized enzymes to catalyze end repair and 3′ A-tailing. This method utilizes SNAP-tagged T4 DNA pol and PNK covalently conjugated to BG-functionalized magnetic beads to carry out end repair of fragmented DNA at 20°C (or 37 °C) for 30 min. The enzymes are removed by magnetic separation from the DNA pool, which is subjected to 3′ A-tailing at 37 °C for 30 min using immobilized Taq DNA pol. ( c ) Streamlined protocol for Illumina amplification-free library preparation using soluble enzymes. Typically, end repair and 3′ A-tailing of fragmented DNA are catalyzed by an enzyme mixture at 20 °C for 30 min, followed by heat treatment at 65 °C for 30 min. ( d ) The workflow of Illumina TruSeq DNA PCR-free LT Library Prep Kit with a purification step. End repair is performed for 30 min at 30 °C, followed by a bead-based step for clean up and size selection. 3′ A-tailing is carried out for 30 min at 37 °C with a subsequent treatment for 5 min at 70 °C. Each library was ligated to preannealed full-length paired-end Illumina adaptors, size-selected and analyzed, and sequenced on an Illumina sequencing platform.

    Article Snippet: To further assess the utility of the immobilized enzymes method on more challenging samples, we have performed Illumina DNA library construction using human FFPE DNA with or without DNA repair as described previously .

    Techniques: Conjugation Assay, Magnetic Beads, Sequencing, Modification, Amplification, Polymerase Chain Reaction, Purification, Selection

    Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

    Journal: PLoS ONE

    Article Title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection

    doi: 10.1371/journal.pone.0041645

    Figure Lengend Snippet: Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

    Article Snippet: These three mixed RNA samples were subsequently used in cDNA library construction and Illumina deep sequencing.

    Techniques: Sample Prep, cDNA Library Assay, Sequencing, Expressing

    Extreme nanochromosomal fragmentation. Contig14329.0 is shown with coordinates in bp. Predicted genes, coding sequences, and introns are indicated by horizontal green, yellow, and white arrows, respectively. 5′ and 3′ fragmentation sites predicted from telomeric read pairs are indicated by red and navy arrows, respectively, with upward pointing solid arrows for sites predicted by 454 telomeric reads and downward pointing dashed arrows for sites predicted by Illumina telomeric reads. Numbers above/below the arrows indicate the number of telomeric reads found at each site for the two telomeric read sources. Alternative nanochromosome isoforms predicted from the 454 telomeric reads (isoforms B–O) are shown below the main locus, with the number of supporting read pairs next to each form. One additional isoform missed by our prediction method but documented in the 454 telomeric read pairs is indicated in pale green. Since the two fragmentation positions at 3,762 and 3,806 bp are in close proximity to each other, they were treated as a single point during alternative isoform prediction. Additional nanochromosome isoforms that were not detected by 454-telomeric reads, including the full eight-gene nanochromosome, but were detected by Southern blotting are indicated by stars (isoforms A, P, Q, and R). Sequence coverage, indicated by the cyan graph, shows the cumulative DNA amplification for all the nanochromosome isoforms. Sequence coverage is calculated from both Illumina telomereless and telomeric reads; telomeric read pairs appear as twin peaks ∼300 bp apart.

    Journal: PLoS Biology

    Article Title: The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny ChromosomesTantalizing Glimpses into a Fragmented Genome

    doi: 10.1371/journal.pbio.1001473

    Figure Lengend Snippet: Extreme nanochromosomal fragmentation. Contig14329.0 is shown with coordinates in bp. Predicted genes, coding sequences, and introns are indicated by horizontal green, yellow, and white arrows, respectively. 5′ and 3′ fragmentation sites predicted from telomeric read pairs are indicated by red and navy arrows, respectively, with upward pointing solid arrows for sites predicted by 454 telomeric reads and downward pointing dashed arrows for sites predicted by Illumina telomeric reads. Numbers above/below the arrows indicate the number of telomeric reads found at each site for the two telomeric read sources. Alternative nanochromosome isoforms predicted from the 454 telomeric reads (isoforms B–O) are shown below the main locus, with the number of supporting read pairs next to each form. One additional isoform missed by our prediction method but documented in the 454 telomeric read pairs is indicated in pale green. Since the two fragmentation positions at 3,762 and 3,806 bp are in close proximity to each other, they were treated as a single point during alternative isoform prediction. Additional nanochromosome isoforms that were not detected by 454-telomeric reads, including the full eight-gene nanochromosome, but were detected by Southern blotting are indicated by stars (isoforms A, P, Q, and R). Sequence coverage, indicated by the cyan graph, shows the cumulative DNA amplification for all the nanochromosome isoforms. Sequence coverage is calculated from both Illumina telomereless and telomeric reads; telomeric read pairs appear as twin peaks ∼300 bp apart.

    Article Snippet: We did not split contigs with missing spans 400 bp from either end of the contig, as the size selection procedure we employed in the Illumina DNA-sequence library construction eliminated most of the sequence coverage in a 160 bp span starting at 100 bp upstream of telomeres.

    Techniques: Southern Blot, Sequencing, Amplification

    Contribution of the main phylogenetic groups classified at order level in the controls with no OPE addition (x axis) and in the OPE addition treatments (amendment with 200 ng/L final nominal concentration, y axis) to the total abundance (% total 16S rDNA, left panel) and the potential activity (% total rRNA reads, right panel). The values are the average of two replicates. Error bars indicate standard deviation.

    Journal: Scientific Reports

    Article Title: Microbial consumption of organophosphate esters in seawater under phosphorus limited conditions

    doi: 10.1038/s41598-018-36635-2

    Figure Lengend Snippet: Contribution of the main phylogenetic groups classified at order level in the controls with no OPE addition (x axis) and in the OPE addition treatments (amendment with 200 ng/L final nominal concentration, y axis) to the total abundance (% total 16S rDNA, left panel) and the potential activity (% total rRNA reads, right panel). The values are the average of two replicates. Error bars indicate standard deviation.

    Article Snippet: Samples for 16S rRNA and rDNA Illumina MiSeq library construction and for determination of OPEs concentrations were collected 0.5 and 24 hours after addition of seawater.

    Techniques: Concentration Assay, Activity Assay, Standard Deviation

    Contribution of the main phylogenetic groups classified at order level in the controls with no OPE addition (x axis) and in the OPE addition treatments (amendment with 200 ng/L final nominal concentration, y axis) to the total abundance (% total 16S rDNA, left panel) and the potential activity (% total rRNA reads, right panel). The values are the average of two replicates. Error bars indicate standard deviation.

    Journal: Scientific Reports

    Article Title: Microbial consumption of organophosphate esters in seawater under phosphorus limited conditions

    doi: 10.1038/s41598-018-36635-2

    Figure Lengend Snippet: Contribution of the main phylogenetic groups classified at order level in the controls with no OPE addition (x axis) and in the OPE addition treatments (amendment with 200 ng/L final nominal concentration, y axis) to the total abundance (% total 16S rDNA, left panel) and the potential activity (% total rRNA reads, right panel). The values are the average of two replicates. Error bars indicate standard deviation.

    Article Snippet: Samples for 16S rRNA and rDNA Illumina MiSeq library construction and for determination of OPEs concentrations were collected 0.5 and 24 hours after addition of seawater.

    Techniques: Concentration Assay, Activity Assay, Standard Deviation

    Enrichment of A. parvulum and altered mitochondrial proteome define the severity of Crohn's disease. ( a ) Interaction network of differentially abundant OTUs; each node represents an OTU and are sized according to their number of interactions; each edge denotes a significant co-exclusion (red) or co-occurence (grey) relationship between OTUs. Nodes are coloured by their number of significant co-exclusions. ( b ) The qPCR quantification of A. parvulum in control and CD microbiota as a function of disease severity. ΔCt was calculated by subtracting average Ct values of universal 16S rDNA from average Ct values of A. parvulum specific primers ( n =18 for controls, nine for mild CD and seven for moderate and severe CD). ** P

    Journal: Nature Communications

    Article Title: Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn's disease

    doi: 10.1038/ncomms13419

    Figure Lengend Snippet: Enrichment of A. parvulum and altered mitochondrial proteome define the severity of Crohn's disease. ( a ) Interaction network of differentially abundant OTUs; each node represents an OTU and are sized according to their number of interactions; each edge denotes a significant co-exclusion (red) or co-occurence (grey) relationship between OTUs. Nodes are coloured by their number of significant co-exclusions. ( b ) The qPCR quantification of A. parvulum in control and CD microbiota as a function of disease severity. ΔCt was calculated by subtracting average Ct values of universal 16S rDNA from average Ct values of A. parvulum specific primers ( n =18 for controls, nine for mild CD and seven for moderate and severe CD). ** P

    Article Snippet: For the V6 reactions, the PCR cycling conditions were identical to the first PCR reaction described in the 16S rDNA-V6 Illumina library construction ‘Methods' section.

    Techniques: Real-time Polymerase Chain Reaction