zr duet dna rna miniprep kit  (Zymo Research)


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    Name:
    Quick DNA RNA Miniprep
    Description:
    The Quick DNA RNA Miniprep Kit provides a quick method for the isolation of high quality genomic DNA and total RNA from small amounts of cells and tissue The kit isolates both genomic DNA and a broad range of RNA species without the use of phenol Small RNAs e g tRNAs microRNAs can be recovered following a simple adjustment within the RNA isolation protocol – no extra steps are required Both DNA and RNA from up to 5x106 cells can be eluted into volumes as little as 25 µl in less than 15 minutes
    Catalog Number:
    d7001
    Product Aliases:
    ZR-Duet DNA/RNA Miniprep
    Price:
    None
    Applications:
    DNA/RNA Co-Purification
    Size:
    50 units
    Category:
    Life Science Reagents and Media
    Buy from Supplier


    Structured Review

    Zymo Research zr duet dna rna miniprep kit
    Quick DNA RNA Miniprep
    The Quick DNA RNA Miniprep Kit provides a quick method for the isolation of high quality genomic DNA and total RNA from small amounts of cells and tissue The kit isolates both genomic DNA and a broad range of RNA species without the use of phenol Small RNAs e g tRNAs microRNAs can be recovered following a simple adjustment within the RNA isolation protocol – no extra steps are required Both DNA and RNA from up to 5x106 cells can be eluted into volumes as little as 25 µl in less than 15 minutes
    https://www.bioz.com/result/zr duet dna rna miniprep kit/product/Zymo Research
    Average 90 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    zr duet dna rna miniprep kit - by Bioz Stars, 2020-01
    90/100 stars

    Images

    1) Product Images from "Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model"

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model

    Journal: Environmental Health Perspectives

    doi: 10.1289/EHP3281

    Use of qRT-PCR CHART to determine slincR enrichment at the sox9b promoter in 48 -hpf whole embryos treated with 0.1% DMSO or 1 ng / mL TCDD. ( A ) Enrichment of slincR RNA by CHART ( slincR probe) and a nonspecific primer set ( β -actin ). Each condition had 3 biological replicates, where 1 replicate consisted of approximately 500 48 -hpf zebrafish. The qRT-PCR data were first normalized to 1% input control, such that 6.644 cycles (i.e., dilution factor log 2 ( 100 ) ) was subtracted from the cycle threshold value (CT; i.e., number of PCR replication cycles required for the sample signal to exceed background levels) of the diluted input and used to calculate the Δ CT for the two probe sets ( Δ CT = CT [ probe ] − CT [ 1 % input- 6.644 ] ). The RNA yield was calculated using the following equation ( 2 − Δ Δ CT × 100 % ). We assigned samples that did not amplify (no enrichment) a CT value of 40. ( B ) Representative slincR qRT-PCR CHART products from panel (A) run on a 1.2% agarose gel. ( C ) qRT-PCR CHART enrichment of slincR RNA at multiple positions ( − 2042 bp , − 963 bp , and − 502 bp ) downstream of the sox9b transcription start site and 5' untranslated region. Each condition had 3 biological replicates ( n = 3 ), where 1 replicate consisted of approximately 500 48 -hpf zebrafish. Expression values were normalized to 1% input control as described for panel (A), except for DNA fold enrichment. We next adjusted relative to the sense probe ( Δ Δ CT = Δ CT [ s l i n c R -probe ] − Δ CT [ sense -probe ] ), and then fold enrichment was calculated ( 2 − Δ Δ CT ). We assigned samples that did not amplify (no enrichment) a CT value of 40. ( D ) qRT-PCR relative expression of slincR and sox9b mRNA in 48 -hpf whole embryo control and sox9b morphants. Expression values were analyzed with the 2 − Δ Δ CT method and normalized to β -actin , whereas the control morphants served as the calibrator. Each sample represents a pool of 20 embryos, each condition had a minimum of four biological replicates ( n = 4 ), and the data were analyzed using a one-way ANOVA with a Tukey post hoc test ( p
    Figure Legend Snippet: Use of qRT-PCR CHART to determine slincR enrichment at the sox9b promoter in 48 -hpf whole embryos treated with 0.1% DMSO or 1 ng / mL TCDD. ( A ) Enrichment of slincR RNA by CHART ( slincR probe) and a nonspecific primer set ( β -actin ). Each condition had 3 biological replicates, where 1 replicate consisted of approximately 500 48 -hpf zebrafish. The qRT-PCR data were first normalized to 1% input control, such that 6.644 cycles (i.e., dilution factor log 2 ( 100 ) ) was subtracted from the cycle threshold value (CT; i.e., number of PCR replication cycles required for the sample signal to exceed background levels) of the diluted input and used to calculate the Δ CT for the two probe sets ( Δ CT = CT [ probe ] − CT [ 1 % input- 6.644 ] ). The RNA yield was calculated using the following equation ( 2 − Δ Δ CT × 100 % ). We assigned samples that did not amplify (no enrichment) a CT value of 40. ( B ) Representative slincR qRT-PCR CHART products from panel (A) run on a 1.2% agarose gel. ( C ) qRT-PCR CHART enrichment of slincR RNA at multiple positions ( − 2042 bp , − 963 bp , and − 502 bp ) downstream of the sox9b transcription start site and 5' untranslated region. Each condition had 3 biological replicates ( n = 3 ), where 1 replicate consisted of approximately 500 48 -hpf zebrafish. Expression values were normalized to 1% input control as described for panel (A), except for DNA fold enrichment. We next adjusted relative to the sense probe ( Δ Δ CT = Δ CT [ s l i n c R -probe ] − Δ CT [ sense -probe ] ), and then fold enrichment was calculated ( 2 − Δ Δ CT ). We assigned samples that did not amplify (no enrichment) a CT value of 40. ( D ) qRT-PCR relative expression of slincR and sox9b mRNA in 48 -hpf whole embryo control and sox9b morphants. Expression values were analyzed with the 2 − Δ Δ CT method and normalized to β -actin , whereas the control morphants served as the calibrator. Each sample represents a pool of 20 embryos, each condition had a minimum of four biological replicates ( n = 4 ), and the data were analyzed using a one-way ANOVA with a Tukey post hoc test ( p

    Techniques Used: Quantitative RT-PCR, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Expressing

    2) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    3) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    4) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    5) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    6) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    7) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    8) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    9) Product Images from "Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition"

    Article Title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

    Journal: Nature

    doi: 10.1038/nature25964

    Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.
    Figure Legend Snippet: Promoter DNA methylation clustering analysis during germline reprogramming. a) The combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for all genes grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. b-c) Boxplots depicting the combined promoter 5mC/5hmC levels (WGBS, right), promoter 5hmC levels (AbaSeq, centre), or gene expression levels (RNA-Seq, right) in consecutive stages of PGC development for three clusters of genes with either low CpG promoters (LCPs; b) or intermediate CpG promoters (ICPs; c) grouped by K-means clustering of the combined 5mC/5hmC dynamics at their promoter regions. For all boxplots, the upper and lower hinges correspond to the first and third quartiles, the middle line corresponds to the median, and the maxima and minima respectively correspond to the highest or lowest value within 1.5× the inter-quartile range. Specific details regarding sample sizes and how samples were collected are found in Statistics and Reproducibility section.

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay, Pyrolysis Gas Chromatography

    DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value
    Figure Legend Snippet: DNA modification and expression dynamics in wild type and Tet1 -KO PGCs at retrotransposons normally activated concurrent with epigenetic reprogramming. a-b) Combined 5mC/5hmC dynamics in wild type PGCs (%; WGBS; far left), relative 5hmC dynamics (AbaSeq read counts normalised to E10.5; centre left) in wild type PGCs, the expression dynamics in either wild type or Tet1 -KO PGCs (transcripts per million (TPM); RNA-Seq; centre right), and combined 5mC/5hmC dynamics in wild type and Tet1 -KO PGCs (%; RRBS; far right) for representative repetitive elements significantly up-regulated (adj. p-value

    Techniques Used: Modification, Expressing, RNA Sequencing Assay

    10) Product Images from "Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice"

    Article Title: Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice

    Journal: Nature Communications

    doi: 10.1038/s41467-017-01944-z

    Ancestral TBT exposure leads to altered DNA methylation and expression of the leptin gene. a Upper panel represents isoDMB #1626 (black bar), and its overlap with regions with different GC content. DMRs punctuating this hypomethylated isoDMB are represented with black vertical bars and numbered (1–2). Overexpressed genes within the isoDMB (Lep, leptin) are represented in green and genes whose expression does not change between DMSO and TBT are represented in gray. b Bottom panels show the variation for the mean ( n = 4) of MBD-seq read coverage for TBT and DMSO samples within 3000 bp regions with the 100 bp DMRs indicated with an asterisk. c RPKMs from RNA-seq analysis of leptin mRNA expression ( n = 4). D, DMSO; T, TBT. Statistical significance was determined using R (version 3.3), and Bioconductor (version 3.3) package edgeR (version 3.14) 54 . Data are presented as mean ± s.e.m. *p
    Figure Legend Snippet: Ancestral TBT exposure leads to altered DNA methylation and expression of the leptin gene. a Upper panel represents isoDMB #1626 (black bar), and its overlap with regions with different GC content. DMRs punctuating this hypomethylated isoDMB are represented with black vertical bars and numbered (1–2). Overexpressed genes within the isoDMB (Lep, leptin) are represented in green and genes whose expression does not change between DMSO and TBT are represented in gray. b Bottom panels show the variation for the mean ( n = 4) of MBD-seq read coverage for TBT and DMSO samples within 3000 bp regions with the 100 bp DMRs indicated with an asterisk. c RPKMs from RNA-seq analysis of leptin mRNA expression ( n = 4). D, DMSO; T, TBT. Statistical significance was determined using R (version 3.3), and Bioconductor (version 3.3) package edgeR (version 3.14) 54 . Data are presented as mean ± s.e.m. *p

    Techniques Used: DNA Methylation Assay, Expressing, RNA Sequencing Assay

    11) Product Images from "Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling"

    Article Title: Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling

    Journal: The ISME Journal

    doi: 10.1038/ismej.2016.40

    Identification of differentially abundant NOGs at the level of DNA and transcription. ( a ) Overlap of NOGs detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for NOGs detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P
    Figure Legend Snippet: Identification of differentially abundant NOGs at the level of DNA and transcription. ( a ) Overlap of NOGs detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for NOGs detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P

    Techniques Used: DNA Sequencing, RNA Sequencing Assay

    Differentially abundant genera in colitis versus steady state. ( a ) Overlap of genera detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for genera detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P
    Figure Legend Snippet: Differentially abundant genera in colitis versus steady state. ( a ) Overlap of genera detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for genera detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P

    Techniques Used: DNA Sequencing, RNA Sequencing Assay

    12) Product Images from "Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling"

    Article Title: Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling

    Journal: The ISME Journal

    doi: 10.1038/ismej.2016.40

    Identification of differentially abundant NOGs at the level of DNA and transcription. ( a ) Overlap of NOGs detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for NOGs detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P
    Figure Legend Snippet: Identification of differentially abundant NOGs at the level of DNA and transcription. ( a ) Overlap of NOGs detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for NOGs detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P

    Techniques Used: DNA Sequencing, RNA Sequencing Assay

    Differentially abundant genera in colitis versus steady state. ( a ) Overlap of genera detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for genera detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P
    Figure Legend Snippet: Differentially abundant genera in colitis versus steady state. ( a ) Overlap of genera detected with ⩾1 read in ⩾1 sample in metagenomic and metatranscriptomic analyses. ( b ) Distributions of reads per million (RPM) for genera detected in DNA-seq, RNA-seq or both data sets (average across 16 samples). *Wilcoxon rank-sum test P

    Techniques Used: DNA Sequencing, RNA Sequencing Assay

    13) Product Images from "Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications"

    Article Title: Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0187636

    Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA and RNA-only Operational Taxonomic Units (OTUs) in all samples, as well as in samples from yachts and motorboats. Numbers in brackets correspond to the number of OTUs in each group.
    Figure Legend Snippet: Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA and RNA-only Operational Taxonomic Units (OTUs) in all samples, as well as in samples from yachts and motorboats. Numbers in brackets correspond to the number of OTUs in each group.

    Techniques Used:

    Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA, and RNA-only Operational Taxonomic Units (OTUs) in individual pairs of eDNA and eRNA samples. Numbers in brackets correspond to the number of OTUs in each group. Samples from either yachts ( Y ) or motorboats ( MB ) are indicated.
    Figure Legend Snippet: Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA, and RNA-only Operational Taxonomic Units (OTUs) in individual pairs of eDNA and eRNA samples. Numbers in brackets correspond to the number of OTUs in each group. Samples from either yachts ( Y ) or motorboats ( MB ) are indicated.

    Techniques Used:

    Global biodiversity of Operational Taxonomic Units (OTUs) for the DNA-only, shared eDNA/eRNA, and RNA-only datasets. The charts show the relative abundance of sequences at highest assigned taxonomic levels.
    Figure Legend Snippet: Global biodiversity of Operational Taxonomic Units (OTUs) for the DNA-only, shared eDNA/eRNA, and RNA-only datasets. The charts show the relative abundance of sequences at highest assigned taxonomic levels.

    Techniques Used:

    14) Product Images from "An epigenetic mechanism for cavefish eye degeneration"

    Article Title: An epigenetic mechanism for cavefish eye degeneration

    Journal: Nature ecology & evolution

    doi: 10.1038/s41559-018-0569-4

    Gene expression changes in cave versus surface fish morphs of Astyanax mexicanus a , Diagram showing the workflow for obtaining larval eyes from A. mexicanus and for co-isolating eye DNA and RNA for whole genome assessment of DNA methylation and gene expression, respectively. b , Percent relative expression of dnmt3bb.1 in the eyes of A. mexicanus cave vs. surface fish morphs by comparison of their respective RNAseq data sets (2-replicates), normalized to surface fish levels, FPKM p
    Figure Legend Snippet: Gene expression changes in cave versus surface fish morphs of Astyanax mexicanus a , Diagram showing the workflow for obtaining larval eyes from A. mexicanus and for co-isolating eye DNA and RNA for whole genome assessment of DNA methylation and gene expression, respectively. b , Percent relative expression of dnmt3bb.1 in the eyes of A. mexicanus cave vs. surface fish morphs by comparison of their respective RNAseq data sets (2-replicates), normalized to surface fish levels, FPKM p

    Techniques Used: Expressing, Fluorescence In Situ Hybridization, DNA Methylation Assay

    15) Product Images from "An epigenetic mechanism for cavefish eye degeneration"

    Article Title: An epigenetic mechanism for cavefish eye degeneration

    Journal: Nature ecology & evolution

    doi: 10.1038/s41559-018-0569-4

    Gene expression changes in cave versus surface fish morphs of Astyanax mexicanus a , Diagram showing the workflow for obtaining larval eyes from A. mexicanus and for co-isolating eye DNA and RNA for whole genome assessment of DNA methylation and gene expression, respectively. b , Percent relative expression of dnmt3bb.1 in the eyes of A. mexicanus cave vs. surface fish morphs by comparison of their respective RNAseq data sets (2-replicates), normalized to surface fish levels, FPKM p
    Figure Legend Snippet: Gene expression changes in cave versus surface fish morphs of Astyanax mexicanus a , Diagram showing the workflow for obtaining larval eyes from A. mexicanus and for co-isolating eye DNA and RNA for whole genome assessment of DNA methylation and gene expression, respectively. b , Percent relative expression of dnmt3bb.1 in the eyes of A. mexicanus cave vs. surface fish morphs by comparison of their respective RNAseq data sets (2-replicates), normalized to surface fish levels, FPKM p

    Techniques Used: Expressing, Fluorescence In Situ Hybridization, DNA Methylation Assay

    16) Product Images from "An epigenetic mechanism for cavefish eye degeneration"

    Article Title: An epigenetic mechanism for cavefish eye degeneration

    Journal: Nature ecology & evolution

    doi: 10.1038/s41559-018-0569-4

    Gene expression changes in cave versus surface fish morphs of Astyanax mexicanus a , Diagram showing the workflow for obtaining larval eyes from A. mexicanus and for co-isolating eye DNA and RNA for whole genome assessment of DNA methylation and gene expression, respectively. b , Percent relative expression of dnmt3bb.1 in the eyes of A. mexicanus cave vs. surface fish morphs by comparison of their respective RNAseq data sets (2-replicates), normalized to surface fish levels, FPKM p
    Figure Legend Snippet: Gene expression changes in cave versus surface fish morphs of Astyanax mexicanus a , Diagram showing the workflow for obtaining larval eyes from A. mexicanus and for co-isolating eye DNA and RNA for whole genome assessment of DNA methylation and gene expression, respectively. b , Percent relative expression of dnmt3bb.1 in the eyes of A. mexicanus cave vs. surface fish morphs by comparison of their respective RNAseq data sets (2-replicates), normalized to surface fish levels, FPKM p

    Techniques Used: Expressing, Fluorescence In Situ Hybridization, DNA Methylation Assay

    17) Product Images from "A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells"

    Article Title: A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw942

    GC content and dinucleotide composition are associated with regulatory activity in U87 cells and hNPCs. ( A, D ) Distributions of expression values for all cis- regulatory elements in U87 cells (A) and hNPCs (D). Expression values are averaged across the three biological replicates and plotted as log 2 (RNA read count/DNA read count). ( B, E ) Box plots displaying GC content for high and low activities cis- regulatory elements in U87 cells (B) and hNPCs (E). GC content is significantly different between high- and low-activity elements in both cell types ( P
    Figure Legend Snippet: GC content and dinucleotide composition are associated with regulatory activity in U87 cells and hNPCs. ( A, D ) Distributions of expression values for all cis- regulatory elements in U87 cells (A) and hNPCs (D). Expression values are averaged across the three biological replicates and plotted as log 2 (RNA read count/DNA read count). ( B, E ) Box plots displaying GC content for high and low activities cis- regulatory elements in U87 cells (B) and hNPCs (E). GC content is significantly different between high- and low-activity elements in both cell types ( P

    Techniques Used: Activity Assay, Expressing

    Quantitative LV-MPRA expression measurements are reproducible. ( A ) Putative cis -regulatory elements cloned upstream of an Hspa1b minimal promoter drive expression of dsRed containing DNA sequence barcodes in the 3΄ UTR. 2600 unique reporter gene constructs were cloned in parallel and the complex lentiviral plasmid library was used to produce lentivirus for transduction. U87 cells and human neural progenitor cells were transduced in triplicate and RNA/DNA were extracted after 96 h in culture. ( B ) Scatter plot showing expression measurements for cis -regulatory elements from two biological replicates in U87 cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.70. ( C ) Scatter plot from two biological replicates in human neural progenitor cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.63.
    Figure Legend Snippet: Quantitative LV-MPRA expression measurements are reproducible. ( A ) Putative cis -regulatory elements cloned upstream of an Hspa1b minimal promoter drive expression of dsRed containing DNA sequence barcodes in the 3΄ UTR. 2600 unique reporter gene constructs were cloned in parallel and the complex lentiviral plasmid library was used to produce lentivirus for transduction. U87 cells and human neural progenitor cells were transduced in triplicate and RNA/DNA were extracted after 96 h in culture. ( B ) Scatter plot showing expression measurements for cis -regulatory elements from two biological replicates in U87 cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.70. ( C ) Scatter plot from two biological replicates in human neural progenitor cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.63.

    Techniques Used: Expressing, Clone Assay, Sequencing, Construct, Plasmid Preparation, Transduction

    Different DNA motifs are enriched in high expressing cis- regulatory elements in U87 cells and hNPCs. ( A ) Scatter plot showing average expression measurements for regulatory elements in U87 cells and hNPCs. Expression in each cell type is plotted as log 2 (RNA read count/DNA read count). Activity in the two cell types is significantly negatively correlated ( R = −0.326, P = 5.02e−53, Pearson's product-moment correlation). ( B ) AME analysis identified motifs enriched in regulatory elements with high activity in U87 cells relative to elements with high activity in hNPCs. ( C ) Motif enrichment in hNPC High Elements relative to U87 High Elements. Motifs enriched in U87 cells ( P
    Figure Legend Snippet: Different DNA motifs are enriched in high expressing cis- regulatory elements in U87 cells and hNPCs. ( A ) Scatter plot showing average expression measurements for regulatory elements in U87 cells and hNPCs. Expression in each cell type is plotted as log 2 (RNA read count/DNA read count). Activity in the two cell types is significantly negatively correlated ( R = −0.326, P = 5.02e−53, Pearson's product-moment correlation). ( B ) AME analysis identified motifs enriched in regulatory elements with high activity in U87 cells relative to elements with high activity in hNPCs. ( C ) Motif enrichment in hNPC High Elements relative to U87 High Elements. Motifs enriched in U87 cells ( P

    Techniques Used: Expressing, Activity Assay

    18) Product Images from "Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications"

    Article Title: Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0187636

    Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA and RNA-only Operational Taxonomic Units (OTUs) in all samples, as well as in samples from yachts and motorboats. Numbers in brackets correspond to the number of OTUs in each group.
    Figure Legend Snippet: Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA and RNA-only Operational Taxonomic Units (OTUs) in all samples, as well as in samples from yachts and motorboats. Numbers in brackets correspond to the number of OTUs in each group.

    Techniques Used:

    Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA, and RNA-only Operational Taxonomic Units (OTUs) in individual pairs of eDNA and eRNA samples. Numbers in brackets correspond to the number of OTUs in each group. Samples from either yachts ( Y ) or motorboats ( MB ) are indicated.
    Figure Legend Snippet: Venn diagrams showing the percentage of DNA-only, shared eDNA/eRNA, and RNA-only Operational Taxonomic Units (OTUs) in individual pairs of eDNA and eRNA samples. Numbers in brackets correspond to the number of OTUs in each group. Samples from either yachts ( Y ) or motorboats ( MB ) are indicated.

    Techniques Used:

    Global biodiversity of Operational Taxonomic Units (OTUs) for the DNA-only, shared eDNA/eRNA, and RNA-only datasets. The charts show the relative abundance of sequences at highest assigned taxonomic levels.
    Figure Legend Snippet: Global biodiversity of Operational Taxonomic Units (OTUs) for the DNA-only, shared eDNA/eRNA, and RNA-only datasets. The charts show the relative abundance of sequences at highest assigned taxonomic levels.

    Techniques Used:

    Related Articles

    GWAS:

    Article Title: Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure
    Article Snippet: Validation For validation of candidate SNPs identified in our GWAS, gene expression was measured following Abamectin exposure on a new set of individuals that were randomly sampled from the population. .. Embryos from wells of interest (Affected and Unaffected) were independently snap frozen using liquid nitrogen and then copurified for RNA and DNA using ZR-Duet™ MiniPrep (Cat #D7001; Zymo Research).

    Filtration:

    Article Title: Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs
    Article Snippet: The ZR-Duet™ DNA/RNA miniprep kit (Zymo Research, Cat# D7001) was used to extract DNA and RNA from 200uL of plasma. .. Pre-extraction steps included spinning the samples at 1600g for 15 minutes at 4°C to remove debris (e.g., insoluble complexes) followed by filtration using 0.2µM syringe filters (Millex® Syringe Filter, Cat# SLGV004SL).

    Polymerase Chain Reaction:

    Article Title: Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature
    Article Snippet: DNA was extracted using ZR-Duet DNA/RNA MiniPrep (Zymo) kits according to the manufacturer’s instructions. .. To assess for the presence of plasmid or EBV genome in iPSCs, PCR was performed using the genomic DNA collected from the iPSCs as template (collected at the same time as expression measurements) with primers designed to amplify the 3’ end of the EBNA-1 gene (present in both the EBV genome and all reprogramming plasmids) and NEBNext High-Fidelity 2X PCR Master Mix.

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions. .. Both the cDNA and genomic DNA enrichment were diluted at 1:20 and were analyzed with primers targeting the slincR transcript and sox9b locus via qRT-PCR using SYBR® green PCR master mix (Thermo Fisher Scientific, cat. no. 4312704) according to manufacturer's instructions.

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: Frozen tissues ( n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. For specimens contaminated with strong melanin content, OneStep PCR Inhibitor Removal Kit (Zymo research) was used for melanin removal.

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: DNA extraction Frozen tissues (n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. For specimens contaminated with strong melanin content, OneStep PCR Inhibitor Removal Kit (Zymo research) was used for melanin removal.

    Picogreen Assay:

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: Frozen tissues ( n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. DNA was quantified using UV spectrophotometer (BioTek, Winooski, VT) and Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific, Carlsbad, CA).

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: DNA extraction Frozen tissues (n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. DNA was quantified using UV spectrophotometer (BioTek, Winooski, VT) and Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific, Carlsbad, CA).

    Quantitative RT-PCR:

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: Paragraph title: qRT-PCR CHART. ... The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions.

    Real-time Polymerase Chain Reaction:

    Article Title: Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure
    Article Snippet: At 120 hpf, 84 individuals (balanced between control, Affected, and Unaffected) were randomly selected for real-time polymerase chain reaction (RT-PCR) gene expression analysis. .. Embryos from wells of interest (Affected and Unaffected) were independently snap frozen using liquid nitrogen and then copurified for RNA and DNA using ZR-Duet™ MiniPrep (Cat #D7001; Zymo Research).

    Article Title: Impact of Low Dose Oral Exposure to Bisphenol A (BPA) on the Neonatal Rat Hypothalamic and Hippocampal Transcriptome: A CLARITY-BPA Consortium Study
    Article Snippet: Paragraph title: Quantitative real-time PCR ... A DNA/RNA miniprep copurification kit (catalog D7001; Zymo Research) with the addition of an on-column DNase I digestion (catalog E1007; Zymo Research) was used to extract RNA.

    Article Title: GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer
    Article Snippet: Nucleic acid from the frozen cell pellets corresponding to each MTS assay was isolated using the ZR-Duet DNA/RNA MiniPrep kit (Zymo Research, # D7001) or separately using Qiagen DNA and RNA isolation kits. .. DNA bisulfite conversion was performed using the EZ DNA Methylation kit and MSP was performed as described above. cDNA was prepared from the isolated RNA using the iScript cDNA synthesis kit and qPCR was performed as described above.

    Incubation:

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: The samples were de-cross-linked using proteinase K (Ambion™, Thermo Fisher Scientific, cat. no. AM2548) and incubated at 55°C for 1 h, followed by 1 h and 40 min at 65°C. .. The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions.

    Article Title: GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer
    Article Snippet: After 48 h of incubation with oxaliplatin, the MTS in vitro cytotoxic assays were performed. .. Nucleic acid from the frozen cell pellets corresponding to each MTS assay was isolated using the ZR-Duet DNA/RNA MiniPrep kit (Zymo Research, # D7001) or separately using Qiagen DNA and RNA isolation kits.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: Frozen tissues ( n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. DNA extraction from formalin-fixed paraffin-embedded (FFPE) specimens ( n = 27) was performed using ZR FFPE DNA MiniPrep (Zymo Research), as previously described [ ].

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: DNA extraction Frozen tissues (n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. DNA extraction from formalin-fixed paraffin-embedded (FFPE) specimens (n = 27) was performed using ZR FFPE DNA MiniPrep (Zymo Research), as previously described [ ].

    Activity Assay:

    Article Title: Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung
    Article Snippet: The above procedure involves the use of high concentration of ethanol designed to prevent the activity of RNase, and ensure high quality RNA (RIN > 7) upon extraction from the LCM samples. .. Microdissected specimens were dropped into a combined DNA/RNA lysis buffer (ZR-Duet™ DNA/RNA MiniPrep, Zymo research, Catalog number: D7001), and stored at −80°C until use.

    Expressing:

    Article Title: Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure
    Article Snippet: At 120 hpf, 84 individuals (balanced between control, Affected, and Unaffected) were randomly selected for real-time polymerase chain reaction (RT-PCR) gene expression analysis. .. Embryos from wells of interest (Affected and Unaffected) were independently snap frozen using liquid nitrogen and then copurified for RNA and DNA using ZR-Duet™ MiniPrep (Cat #D7001; Zymo Research).

    Article Title: Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature
    Article Snippet: DNA was extracted using ZR-Duet DNA/RNA MiniPrep (Zymo) kits according to the manufacturer’s instructions. .. To assess for the presence of plasmid or EBV genome in iPSCs, PCR was performed using the genomic DNA collected from the iPSCs as template (collected at the same time as expression measurements) with primers designed to amplify the 3’ end of the EBNA-1 gene (present in both the EBV genome and all reprogramming plasmids) and NEBNext High-Fidelity 2X PCR Master Mix.

    Article Title: Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo[a]pyrene in zebrafish
    Article Snippet: To isolate both RNA and DNA from the same biological samples, the Zymo ZR-Duet MiniPrep (Zymo Research, Irvine, CA, Product #: D7001) was used from pools of n=8 zebrafish at both 24 and 120 hpf, according to manufacturer protocol. .. Two-way ANOVA was used to determine the effect of treatment and time on Dnmt expression (p < 0.05).

    Hybridization:

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: The control probe comprised of the sense sequence of the same region, and the input samples did not contain a hybridization probe. .. The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions.

    Cell Culture:

    Article Title: Epigenetic regulation of OAS2 shows disease-specific DNA methylation profiles at individual CpG sites
    Article Snippet: Paragraph title: Cell culture and stimuli ... Cells were collected 24 hours after stimulation and RNA/DNA co-isolated using ZR-Duet™ DNA/RNA MiniPrep from Zymo Research, according to the manufacturer’s manual (Irvine, CA, USA).

    Generated:

    Article Title: Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature
    Article Snippet: Briefly, embryoid bodies were generated by manual colony detachment and were grown in suspension for seven days on low adherent plates in bFGF-free hESC media. .. DNA was extracted using ZR-Duet DNA/RNA MiniPrep (Zymo) kits according to the manufacturer’s instructions.

    Sequencing:

    Article Title: A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees
    Article Snippet: Paragraph title: RNA-seq library preparation and sequencing ... Extractions were performed in ten species-balanced batches using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA).

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: The control probe comprised of the sense sequence of the same region, and the input samples did not contain a hybridization probe. .. The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions.

    Sonication:

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: Further, 108 pmol of a 60 -bp biotin-labeled capture probe targeting exon 1 of slincR was added to 100 μ L of the sonication solution and incubated overnight at room temperature on an end-over-end rotator. .. The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions.

    Copurification:

    Article Title: Impact of Low Dose Oral Exposure to Bisphenol A (BPA) on the Neonatal Rat Hypothalamic and Hippocampal Transcriptome: A CLARITY-BPA Consortium Study
    Article Snippet: .. A DNA/RNA miniprep copurification kit (catalog D7001; Zymo Research) with the addition of an on-column DNase I digestion (catalog E1007; Zymo Research) was used to extract RNA. .. Extracted DNA was sent to another CLARITY consortium member for independent analysis. mRNA was reverse transcribed to single-strand complementary cDNA with the high capacity RNA-to-cDNA kit (catalog 4387406; Applied Biosystems).

    MTS Assay:

    Article Title: GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer
    Article Snippet: .. Nucleic acid from the frozen cell pellets corresponding to each MTS assay was isolated using the ZR-Duet DNA/RNA MiniPrep kit (Zymo Research, # D7001) or separately using Qiagen DNA and RNA isolation kits. .. DNA bisulfite conversion was performed using the EZ DNA Methylation kit and MSP was performed as described above. cDNA was prepared from the isolated RNA using the iScript cDNA synthesis kit and qPCR was performed as described above.

    DNA Extraction:

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: Paragraph title: DNA extraction ... Frozen tissues ( n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol.

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: .. DNA extraction Frozen tissues (n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. DNA extraction from formalin-fixed paraffin-embedded (FFPE) specimens (n = 27) was performed using ZR FFPE DNA MiniPrep (Zymo Research), as previously described [ ].

    RNA Sequencing Assay:

    Article Title: Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
    Article Snippet: .. RNA-seq RNA was extracted from ~3 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA) in two species-balanced batches. ..

    Article Title: A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees
    Article Snippet: Paragraph title: RNA-seq library preparation and sequencing ... Extractions were performed in ten species-balanced batches using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA).

    Article Title: Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
    Article Snippet: Paragraph title: RNA-seq ... RNA was extracted from ~3 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA) in two species-balanced batches.

    Methylation:

    Article Title: Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo[a]pyrene in zebrafish
    Article Snippet: To isolate both RNA and DNA from the same biological samples, the Zymo ZR-Duet MiniPrep (Zymo Research, Irvine, CA, Product #: D7001) was used from pools of n=8 zebrafish at both 24 and 120 hpf, according to manufacturer protocol. .. The DNA samples were eluted and used in the MethylFlash™ Global DNA Methylation Quantification Kit (Epigentek Group, Farmingdale, NY, Product # P-2094) to quantify the percent of methylated cytosine in the genomic DNA.

    Isolation:

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: .. The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions. .. To determine slincR enrichment, 2 μ L of RNA pull down was converted to cDNA using a SuperScript™ VILO™ cDNA synthesis kit (Thermo Fisher Scientific, cat. no. 11754050) according to manufacturer's instructions.

    Article Title: GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer
    Article Snippet: .. Nucleic acid from the frozen cell pellets corresponding to each MTS assay was isolated using the ZR-Duet DNA/RNA MiniPrep kit (Zymo Research, # D7001) or separately using Qiagen DNA and RNA isolation kits. .. DNA bisulfite conversion was performed using the EZ DNA Methylation kit and MSP was performed as described above. cDNA was prepared from the isolated RNA using the iScript cDNA synthesis kit and qPCR was performed as described above.

    Article Title: Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs
    Article Snippet: The ZR-Duet™ DNA/RNA miniprep kit (Zymo Research, Cat# D7001) was used to extract DNA and RNA from 200uL of plasma. .. The kit isolated and purified DNA and RNA separately without the use of carrier RNA.

    Size-exclusion Chromatography:

    Article Title: Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung
    Article Snippet: The slide-mounted frozen sections were then fixed by placement in 75% ethanol for 30 sec, and then were immediately stained for 1 min with staining solution (staining solution: 2.8% cresyl violet, 0.15% eosin Y, and 70% ethanol), and were dehydrated by a series of 75% ethanol (30 sec), 75% ethanol (20 dips), 95% ethanol (30 s), 100% ethanol (1 min), 100% ethanol (1 min), and xylene (5 min) treatments. .. Microdissected specimens were dropped into a combined DNA/RNA lysis buffer (ZR-Duet™ DNA/RNA MiniPrep, Zymo research, Catalog number: D7001), and stored at −80°C until use.

    Purification:

    Article Title: Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs
    Article Snippet: The ZR-Duet™ DNA/RNA miniprep kit (Zymo Research, Cat# D7001) was used to extract DNA and RNA from 200uL of plasma. .. The kit isolated and purified DNA and RNA separately without the use of carrier RNA.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure
    Article Snippet: At 120 hpf, 84 individuals (balanced between control, Affected, and Unaffected) were randomly selected for real-time polymerase chain reaction (RT-PCR) gene expression analysis. .. Embryos from wells of interest (Affected and Unaffected) were independently snap frozen using liquid nitrogen and then copurified for RNA and DNA using ZR-Duet™ MiniPrep (Cat #D7001; Zymo Research).

    Lysis:

    Article Title: Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung
    Article Snippet: .. Microdissected specimens were dropped into a combined DNA/RNA lysis buffer (ZR-Duet™ DNA/RNA MiniPrep, Zymo research, Catalog number: D7001), and stored at −80°C until use. .. Peripheral blood T lymphocytes were isolated using the Pan T Cell Isolation Kit (Miltenyi Biotec, Inc.) from peripheral blood mononuclear cell (PBMC) by the Molecular Cytogenetic Core of Department of Genetics, Albert Einstein College of Medicine.

    Plasmid Preparation:

    Article Title: Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature
    Article Snippet: DNA was extracted using ZR-Duet DNA/RNA MiniPrep (Zymo) kits according to the manufacturer’s instructions. .. To assess for the presence of plasmid or EBV genome in iPSCs, PCR was performed using the genomic DNA collected from the iPSCs as template (collected at the same time as expression measurements) with primers designed to amplify the 3’ end of the EBNA-1 gene (present in both the EBV genome and all reprogramming plasmids) and NEBNext High-Fidelity 2X PCR Master Mix.

    SYBR Green Assay:

    Article Title: Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model
    Article Snippet: The enriched DNA and RNA were isolated using the ZYMO ZR-Duet™ DNA/RNA miniprep kit (cat. no. D7001) according to manufacturer's instructions. .. Both the cDNA and genomic DNA enrichment were diluted at 1:20 and were analyzed with primers targeting the slincR transcript and sox9b locus via qRT-PCR using SYBR® green PCR master mix (Thermo Fisher Scientific, cat. no. 4312704) according to manufacturer's instructions.

    In Vitro:

    Article Title: GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer
    Article Snippet: After 48 h of incubation with oxaliplatin, the MTS in vitro cytotoxic assays were performed. .. Nucleic acid from the frozen cell pellets corresponding to each MTS assay was isolated using the ZR-Duet DNA/RNA MiniPrep kit (Zymo Research, # D7001) or separately using Qiagen DNA and RNA isolation kits.

    Laser Capture Microdissection:

    Article Title: Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung
    Article Snippet: Paragraph title: Tissue handling and laser capture microdissection (LCM) of human lung ... Microdissected specimens were dropped into a combined DNA/RNA lysis buffer (ZR-Duet™ DNA/RNA MiniPrep, Zymo research, Catalog number: D7001), and stored at −80°C until use.

    Spectrophotometry:

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: Frozen tissues ( n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. DNA was quantified using UV spectrophotometer (BioTek, Winooski, VT) and Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific, Carlsbad, CA).

    Article Title: Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
    Article Snippet: DNA extraction Frozen tissues (n = 62) were homogenized with a sonicator and filtered using QIAshredder (QIAGEN, Valencia, CA), and DNA was extracted using the ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA), according to the manufacturer’s protocol. .. DNA was quantified using UV spectrophotometer (BioTek, Winooski, VT) and Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific, Carlsbad, CA).

    DNA Methylation Assay:

    Article Title: GPX3 promoter methylation predicts platinum sensitivity in colorectal cancer
    Article Snippet: Nucleic acid from the frozen cell pellets corresponding to each MTS assay was isolated using the ZR-Duet DNA/RNA MiniPrep kit (Zymo Research, # D7001) or separately using Qiagen DNA and RNA isolation kits. .. DNA bisulfite conversion was performed using the EZ DNA Methylation kit and MSP was performed as described above. cDNA was prepared from the isolated RNA using the iScript cDNA synthesis kit and qPCR was performed as described above.

    Article Title: Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo[a]pyrene in zebrafish
    Article Snippet: Paragraph title: Quantification of Global DNA Methylation ... To isolate both RNA and DNA from the same biological samples, the Zymo ZR-Duet MiniPrep (Zymo Research, Irvine, CA, Product #: D7001) was used from pools of n=8 zebrafish at both 24 and 120 hpf, according to manufacturer protocol.

    Concentration Assay:

    Article Title: A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees
    Article Snippet: Extractions were performed in ten species-balanced batches using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA). .. RNA concentration and quality was measured using the Agilent 2100 Bioanalyzer.

    Article Title: Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung
    Article Snippet: The above procedure involves the use of high concentration of ethanol designed to prevent the activity of RNase, and ensure high quality RNA (RIN > 7) upon extraction from the LCM samples. .. Microdissected specimens were dropped into a combined DNA/RNA lysis buffer (ZR-Duet™ DNA/RNA MiniPrep, Zymo research, Catalog number: D7001), and stored at −80°C until use.

    Staining:

    Article Title: Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature
    Article Snippet: Cells were fixed and stained using antibodies against nestin (1:250 SC-71665, Santa Cruz Biotech), α-smooth muscle actin (1:1500, CBL171, Millipore), alpha-Fetoprotein (1:100, SC-130302, Santa Cruz Biotech), and HNF3β (1:100 SC-6554, Santa Cruz Biotech) to detect ectoderm, mesoderm, and endoderm lineages respectively. .. DNA was extracted using ZR-Duet DNA/RNA MiniPrep (Zymo) kits according to the manufacturer’s instructions.

    Article Title: Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung
    Article Snippet: The slide-mounted frozen sections were then fixed by placement in 75% ethanol for 30 sec, and then were immediately stained for 1 min with staining solution (staining solution: 2.8% cresyl violet, 0.15% eosin Y, and 70% ethanol), and were dehydrated by a series of 75% ethanol (30 sec), 75% ethanol (20 dips), 95% ethanol (30 s), 100% ethanol (1 min), 100% ethanol (1 min), and xylene (5 min) treatments. .. Microdissected specimens were dropped into a combined DNA/RNA lysis buffer (ZR-Duet™ DNA/RNA MiniPrep, Zymo research, Catalog number: D7001), and stored at −80°C until use.

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    Zymo Research zr duet dna rna miniprep plus kit
    Zr Duet Dna Rna Miniprep Plus Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Zymo Research zr duet dna rna extraction kit
    Zr Duet Dna Rna Extraction Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/zr duet dna rna extraction kit/product/Zymo Research
    Average 90 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    zr duet dna rna extraction kit - by Bioz Stars, 2020-01
    90/100 stars
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