parallel dna rna extraction  (Zymo Research)


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    Name:
    Quick DNA RNA Miniprep Plus Kit
    Description:
    The Quick DNA RNA MiniPrep Plus kit combines Quick DNA RNA technology with the addition of DNA RNA Shield a unique preservation and lysis technology and Proteinase K to enable easy reliable and rapid isolation from any biological sample including cells solid tissue and whole blood The procedure uses Zymo Spin column technology that results in high quality genomic DNA and total RNA that is ready for any downstream application including reverse transcription microarray sequencing etc
    Catalog Number:
    d7003
    Product Aliases:
    ZR-Duet DNA/RNA Miniprep Plus
    Price:
    None
    Applications:
    DNA/RNA Co-Purification
    Size:
    50 units
    Category:
    Life Science Reagents and Media
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    Structured Review

    Zymo Research parallel dna rna extraction
    Quick DNA RNA Miniprep Plus Kit
    The Quick DNA RNA MiniPrep Plus kit combines Quick DNA RNA technology with the addition of DNA RNA Shield a unique preservation and lysis technology and Proteinase K to enable easy reliable and rapid isolation from any biological sample including cells solid tissue and whole blood The procedure uses Zymo Spin column technology that results in high quality genomic DNA and total RNA that is ready for any downstream application including reverse transcription microarray sequencing etc
    https://www.bioz.com/result/parallel dna rna extraction/product/Zymo Research
    Average 95 stars, based on 115 article reviews
    Price from $9.99 to $1999.99
    parallel dna rna extraction - by Bioz Stars, 2020-02
    95/100 stars

    Images

    1) Product Images from "Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children"

    Article Title: Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

    Journal: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

    doi: 10.1093/cid/ciy802

    Microbial alignments detected in the lungs of immunocompromised children. Red dots represent potentially pathogenic microbes that are both abundant (≥10 rpm for bacteria or ≥1 rpm for fungi or viruses) and identified at levels greater than most other samples in the cohort (Z-score ≥2). Hollow red dots indicating Bocavirus and Pneumocystis are used to indicate organisms observed only once in this cohort. Blue dots represent all other potentially pathogenic microbes; light blue dots represent typically nonpathogenic microbes. Subplots show (A ) all bacteria, (B ) fungi, (C ) RNA viruses, and (D ) DNA viruses identified across all samples in the cohort. For the purpose of the Z-score calculation, the value of log 10 -transformed reads for undetected microbes was assumed to equal –2, just below the lower limit of detection for our sequencing depth (log 10 [0.01rpm] = –2). Abbreviation: seq, sequencing.
    Figure Legend Snippet: Microbial alignments detected in the lungs of immunocompromised children. Red dots represent potentially pathogenic microbes that are both abundant (≥10 rpm for bacteria or ≥1 rpm for fungi or viruses) and identified at levels greater than most other samples in the cohort (Z-score ≥2). Hollow red dots indicating Bocavirus and Pneumocystis are used to indicate organisms observed only once in this cohort. Blue dots represent all other potentially pathogenic microbes; light blue dots represent typically nonpathogenic microbes. Subplots show (A ) all bacteria, (B ) fungi, (C ) RNA viruses, and (D ) DNA viruses identified across all samples in the cohort. For the purpose of the Z-score calculation, the value of log 10 -transformed reads for undetected microbes was assumed to equal –2, just below the lower limit of detection for our sequencing depth (log 10 [0.01rpm] = –2). Abbreviation: seq, sequencing.

    Techniques Used: Transformation Assay, Sequencing

    2) 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

    3) 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

    4) 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:

    5) 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

    6) Product Images from "Follicular Helper T Cells Are Major Human Immunodeficiency Virus-2 Reservoirs and Support Productive Infection"

    Article Title: Follicular Helper T Cells Are Major Human Immunodeficiency Virus-2 Reservoirs and Support Productive Infection

    Journal: The Journal of Infectious Diseases

    doi: 10.1093/infdis/jiz431

    In vitro infection of tonsillar follicular helper T cells (Tfh) by human immunodeficiency virus (HIV)-2. (A) Illustrative dot plots of the sorting strategy, based on CXCR5, PD-1, and ICOS expression, used to isolate Tfh from human tonsillar mononuclear cells enriched for CD4 T cells by magnetic isolation. (B) Total HIV deoxyribonucleic acid (DNA) and (C) gag messenger ribonucleic acid (mRNA) quantified after 24-hour infection with R5- or X4-tropic HIV-2 or HIV-1 primary isolates. (D) Correlation of total HIV DNA and viral gag mRNA levels. (E) Comparison of total viral DNA at 24 hours postinfection and after 48-hour T-cell receptor (TCR)-mediated stimulation with α-CD3i/α-CD28s. (F) Infectivity of culture supernatants harvested after 48-hour TCR stimulation of HIV-infected Tfh assessed using a TZM-bl reporter cell line and chlorophenolred-β- d -galactopyranoside colorimetric assay (CPRG). Each dot represents 1 independent experiment, and each color refers to a different tonsil donor. * P
    Figure Legend Snippet: In vitro infection of tonsillar follicular helper T cells (Tfh) by human immunodeficiency virus (HIV)-2. (A) Illustrative dot plots of the sorting strategy, based on CXCR5, PD-1, and ICOS expression, used to isolate Tfh from human tonsillar mononuclear cells enriched for CD4 T cells by magnetic isolation. (B) Total HIV deoxyribonucleic acid (DNA) and (C) gag messenger ribonucleic acid (mRNA) quantified after 24-hour infection with R5- or X4-tropic HIV-2 or HIV-1 primary isolates. (D) Correlation of total HIV DNA and viral gag mRNA levels. (E) Comparison of total viral DNA at 24 hours postinfection and after 48-hour T-cell receptor (TCR)-mediated stimulation with α-CD3i/α-CD28s. (F) Infectivity of culture supernatants harvested after 48-hour TCR stimulation of HIV-infected Tfh assessed using a TZM-bl reporter cell line and chlorophenolred-β- d -galactopyranoside colorimetric assay (CPRG). Each dot represents 1 independent experiment, and each color refers to a different tonsil donor. * P

    Techniques Used: In Vitro, Infection, Expressing, Isolation, Colorimetric 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) 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

    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) 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

    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 "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

    11) 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

    12) 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

    13) 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

    14) 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

    15) 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:

    16) 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

    17) 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

    18) 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

    19) 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

    20) 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

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    Cell Isolation:

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    Amplification:

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    Filtration:

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    Immunostaining:

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    Gene Assay:

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    Incubation:

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    Derivative Assay:

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    Northern Blot:

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    Digital PCR:

    Article Title: Microbial colonization is required for normal neurobehavioral development in zebrafish
    Article Snippet: .. Droplet digital PCR (ddPCR) DNA was isolated from 6 dpf and 10 dpf axenic, conventionalized, and conventionally colonized larvae using the ZR-Duet DNA/RNA MiniPrep Plus Kit (Zymo Research #D7003) according to the manufacturer’s protocol. .. The BioRad QX200 Droplet Digital PCR System was used to quantitate 16S rRNA gene copies.

    Generated:

    Article Title: High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
    Article Snippet: SRD5A3 KO hiPSCs clones were generated by CRISPR/Cas9. sgRNA (inserted into a GFP-containing PX458 plasmid, Addgene) targeting the first exon of the gene were generated via the CRISPOR website and validated in T293 HEK cells by Sanger sequencing combined with tides analysis ( https://tide-calculator.nki.nl/ ; data not shown). hiPSCs were transfected by nucleofection (Amaxa 4D, Lonza) and transfected cells (GFP+) were isolated by FACs (BD FACSAria II SORP, BD Biosciences) to generate single-cell-of-origin colonies. .. DNA was extracted from a piece of each colony by ZR-Duet DNA MiniPrep (D7003, Zymo) and sequenced.

    DNA Sequencing:

    Article Title: Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol
    Article Snippet: Paragraph title: DNA sequencing of 16S rRNA gene ... DNA was isolated from each sample using a ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research #D7003).

    Polymerase Chain Reaction:

    Article Title: Studying the microbiota of bats: Accuracy of direct and indirect samplings. Studying the microbiota of bats: Accuracy of direct and indirect samplings
    Article Snippet: 2.2 Sample processing DNA extraction was performed as detailed previously (Dietrich et al., ), using a ZR‐Duet DNA/RNA MiniPrep Plus kit (Zymo Research), and a pre‐treatment for robust lysis of Gram‐positive and Gram‐negative bacteria. .. Eluted DNA was then used for Illumina sequencing of 16S amplicons in a single run, including a negative PCR control to further identify potential exogenous bacterial DNA introduced during library preparation, as described previously (Dietrich et al., ).

    Article Title: Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol
    Article Snippet: DNA was isolated from each sample using a ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research #D7003). .. DNA (250 ng) from each sample was added to triplicate PCR reactions along with barcoded primers specific for the V4 region of the 16S rRNA gene and amplified with the Roche FastStart High Fidelity PCR System (Sigma-Aldrich, #4738292001).

    Article Title: Unexpected Cartilage Phenotype in CD4-Cre-Conditional SOS-Deficient Mice
    Article Snippet: Paragraph title: Purification of CD4+ T Cells/DNA Isolation/Genomic PCR ... Tissue DNA was isolated using DNA columns from a ZR-Duet DNA/RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA).

    Article Title: Detection of Rickettsiae, Borreliae, and Ehrlichiae in Ticks Collected from Walker County, Texas, 2017–2018
    Article Snippet: In addition to morphological identification, the species of nymphal ticks were confirmed by PCR amplification and sequencing approximately 460 bp from the 3′ end of the mitochondrial 16S rRNA gene (rDNA) using primers 16S+1 (5′-CTGCTCAATGATTTTTTAAATTGCTGTGG-3′) and 16S-1 (5′-CCGGTCTGAACTCAGATCAAGT-3′) [ ]. .. DNA and RNA were co-extracted from half of the homogenate using the ZR Duet DNA/RNA MiniPrep Plus Kit (Zymo Research, Irvine, CA, USA), and the remaining homogenate was stored at −80 °C for further evaluation.

    DNA Extraction:

    Article Title: Studying the microbiota of bats: Accuracy of direct and indirect samplings. Studying the microbiota of bats: Accuracy of direct and indirect samplings
    Article Snippet: .. 2.2 Sample processing DNA extraction was performed as detailed previously (Dietrich et al., ), using a ZR‐Duet DNA/RNA MiniPrep Plus kit (Zymo Research), and a pre‐treatment for robust lysis of Gram‐positive and Gram‐negative bacteria. .. We included three negative controls during DNA extraction to control for the presence of exogenous DNA in laboratory reagents and materials.

    Article Title: Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol
    Article Snippet: DNA extraction and sequencing of the 16S rRNA gene was completed as previously described . .. DNA was isolated from each sample using a ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research #D7003).

    Article Title: An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region
    Article Snippet: .. DNA isolation: DNA was extracted using the ZR-Duet DNA/RNA MiniPrep Plus (Zymo Research, Irvine, CA, USA) kit for all coral samples. ..

    Article Title: Unexpected Cartilage Phenotype in CD4-Cre-Conditional SOS-Deficient Mice
    Article Snippet: Non-lymphoid tissues were homogenized prior to DNA isolation using a TissueMiser System, 115 V (Fisher Scientific, Hampton, NH, USA). .. Tissue DNA was isolated using DNA columns from a ZR-Duet DNA/RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA).

    RNA Sequencing Assay:

    Article Title: Genome-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer
    Article Snippet: .. 5 RNA sequencing (RNA-Seq) Total RNA from HCC1806 and MDA-MB-231 cells was extracted using ZR-Duet DNA/RNA MiniPrep Plus (cat# D7003; Zymo Research, Irvine, CA). .. RNA samples with high quality (RIN ≥ 8.0) and high purity (OD 260/280 = 1.8–2.0) scores were used to generate libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, CA).

    RNA HS Assay:

    Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
    Article Snippet: After sorting, gDNA and total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit (#D7003, Zymo Research, Irvine, CA) according to the manufacturer’s instruction. .. After these purification steps, gDNA and total RNA were quantified by Qubit dsDNA HS (#Q32851, ThermoFisher) and RNA HS assay (#Q32852, ThermoFisher) kits, respectively.

    Fluorescence:

    Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
    Article Snippet: Immuno-labeled nuclei were collected as NeuN-positive or OLIG2-positive populations by fluorescence-activated nuclei sorting (FANS). .. After sorting, gDNA and total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit (#D7003, Zymo Research, Irvine, CA) according to the manufacturer’s instruction.

    Multiple Displacement Amplification:

    Article Title: Genome-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer
    Article Snippet: .. 5 RNA sequencing (RNA-Seq) Total RNA from HCC1806 and MDA-MB-231 cells was extracted using ZR-Duet DNA/RNA MiniPrep Plus (cat# D7003; Zymo Research, Irvine, CA). .. RNA samples with high quality (RIN ≥ 8.0) and high purity (OD 260/280 = 1.8–2.0) scores were used to generate libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, CA).

    Isolation:

    Article Title: High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
    Article Snippet: SRD5A3 ; data not shown). hiPSCs were transfected by nucleofection (Amaxa 4D, Lonza) and transfected cells (GFP+) were isolated by FACs (BD FACSAria II SORP, BD Biosciences) to generate single-cell-of-origin colonies. .. DNA was extracted from a piece of each colony by ZR-Duet DNA MiniPrep (D7003, Zymo) and sequenced.

    Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
    Article Snippet: Paragraph title: Nuclei isolation from human postmortem brain ... After sorting, gDNA and total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit (#D7003, Zymo Research, Irvine, CA) according to the manufacturer’s instruction.

    Article Title: Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol
    Article Snippet: .. DNA was isolated from each sample using a ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research #D7003). ..

    Article Title: Unexpected Cartilage Phenotype in CD4-Cre-Conditional SOS-Deficient Mice
    Article Snippet: .. Tissue DNA was isolated using DNA columns from a ZR-Duet DNA/RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA). ..

    Article Title: Detection of Rickettsiae, Borreliae, and Ehrlichiae in Ticks Collected from Walker County, Texas, 2017–2018
    Article Snippet: Half of the ticks were stored at −80 °C for future analysis such as pathogen isolation. .. DNA and RNA were co-extracted from half of the homogenate using the ZR Duet DNA/RNA MiniPrep Plus Kit (Zymo Research, Irvine, CA, USA), and the remaining homogenate was stored at −80 °C for further evaluation.

    Article Title: TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
    Article Snippet: .. RNA isolation, RT-qPCR and northern blot RNA was extracted using Quick-RNA™ MiniPrep (Zymo Research D7003) and DNAse treated in-column either with the DNAse provided on the kit or with the TURBO DNA-free™ Kit (Ambion, AM1907). .. RNA (1 μg) was retrotranscribed using SuperScript® III Reverse Transcriptase (Invitrogen, Cat. 18080044) and the cDNA was diluted 1/10 for qPCRs using MESA BLUE MasterMix (Eurogenentec, 10-SY2X-03 + NRWOUB) on a LightCycler® 480 Instrument II (Roche).

    Article Title: Microbial colonization is required for normal neurobehavioral development in zebrafish
    Article Snippet: .. Droplet digital PCR (ddPCR) DNA was isolated from 6 dpf and 10 dpf axenic, conventionalized, and conventionally colonized larvae using the ZR-Duet DNA/RNA MiniPrep Plus Kit (Zymo Research #D7003) according to the manufacturer’s protocol. .. The BioRad QX200 Droplet Digital PCR System was used to quantitate 16S rRNA gene copies.

    Size-exclusion Chromatography:

    Article Title: Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol
    Article Snippet: DNA was isolated from each sample using a ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research #D7003). .. PCR reactions were run at 95 °C for 2 min, followed by 25 cycles of 95 °C for 30 sec, 55 °C for 30 sec and 72 °C for 1 min, with a 10 min final extension at 72 °C.

    Purification:

    Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
    Article Snippet: .. After sorting, gDNA and total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit (#D7003, Zymo Research, Irvine, CA) according to the manufacturer’s instruction. ..

    Article Title: Unexpected Cartilage Phenotype in CD4-Cre-Conditional SOS-Deficient Mice
    Article Snippet: Paragraph title: Purification of CD4+ T Cells/DNA Isolation/Genomic PCR ... Tissue DNA was isolated using DNA columns from a ZR-Duet DNA/RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA).

    Sequencing:

    Article Title: Studying the microbiota of bats: Accuracy of direct and indirect samplings. Studying the microbiota of bats: Accuracy of direct and indirect samplings
    Article Snippet: 2.2 Sample processing DNA extraction was performed as detailed previously (Dietrich et al., ), using a ZR‐Duet DNA/RNA MiniPrep Plus kit (Zymo Research), and a pre‐treatment for robust lysis of Gram‐positive and Gram‐negative bacteria. .. Eluted DNA was then used for Illumina sequencing of 16S amplicons in a single run, including a negative PCR control to further identify potential exogenous bacterial DNA introduced during library preparation, as described previously (Dietrich et al., ).

    Article Title: High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
    Article Snippet: SRD5A3 KO hiPSCs clones were generated by CRISPR/Cas9. sgRNA (inserted into a GFP-containing PX458 plasmid, Addgene) targeting the first exon of the gene were generated via the CRISPOR website and validated in T293 HEK cells by Sanger sequencing combined with tides analysis ( https://tide-calculator.nki.nl/ ; data not shown). hiPSCs were transfected by nucleofection (Amaxa 4D, Lonza) and transfected cells (GFP+) were isolated by FACs (BD FACSAria II SORP, BD Biosciences) to generate single-cell-of-origin colonies. .. DNA was extracted from a piece of each colony by ZR-Duet DNA MiniPrep (D7003, Zymo) and sequenced.

    Article Title: Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol
    Article Snippet: DNA extraction and sequencing of the 16S rRNA gene was completed as previously described . .. DNA was isolated from each sample using a ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research #D7003).

    Article Title: Genome-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer
    Article Snippet: 5 RNA sequencing (RNA-Seq) Total RNA from HCC1806 and MDA-MB-231 cells was extracted using ZR-Duet DNA/RNA MiniPrep Plus (cat# D7003; Zymo Research, Irvine, CA). .. The mRNA libraries were sequenced on the Illumina HiSeq 2500 in Rapid Mode using 101 bp paired-end reads at the JWCI Sequencing Center .

    Article Title: Detection of Rickettsiae, Borreliae, and Ehrlichiae in Ticks Collected from Walker County, Texas, 2017–2018
    Article Snippet: In addition to morphological identification, the species of nymphal ticks were confirmed by PCR amplification and sequencing approximately 460 bp from the 3′ end of the mitochondrial 16S rRNA gene (rDNA) using primers 16S+1 (5′-CTGCTCAATGATTTTTTAAATTGCTGTGG-3′) and 16S-1 (5′-CCGGTCTGAACTCAGATCAAGT-3′) [ ]. .. DNA and RNA were co-extracted from half of the homogenate using the ZR Duet DNA/RNA MiniPrep Plus Kit (Zymo Research, Irvine, CA, USA), and the remaining homogenate was stored at −80 °C for further evaluation.

    FACS:

    Article Title: High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
    Article Snippet: SRD5A3 ; data not shown). hiPSCs were transfected by nucleofection (Amaxa 4D, Lonza) and transfected cells (GFP+) were isolated by FACs (BD FACSAria II SORP, BD Biosciences) to generate single-cell-of-origin colonies. .. DNA was extracted from a piece of each colony by ZR-Duet DNA MiniPrep (D7003, Zymo) and sequenced.

    Article Title: Discovery of a stem-like multipotent cell fate
    Article Snippet: Paragraph title: FACS sorting & microarray ... All cells were directly sorted into DNA/RNA Shield Buffer from the Zymo Duet DNA/RNA MiniPrep Plus kit (Zymo #D7003), followed by RNA extraction as per provided protocol.

    Quantitative RT-PCR:

    Article Title: TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
    Article Snippet: .. RNA isolation, RT-qPCR and northern blot RNA was extracted using Quick-RNA™ MiniPrep (Zymo Research D7003) and DNAse treated in-column either with the DNAse provided on the kit or with the TURBO DNA-free™ Kit (Ambion, AM1907). .. RNA (1 μg) was retrotranscribed using SuperScript® III Reverse Transcriptase (Invitrogen, Cat. 18080044) and the cDNA was diluted 1/10 for qPCRs using MESA BLUE MasterMix (Eurogenentec, 10-SY2X-03 + NRWOUB) on a LightCycler® 480 Instrument II (Roche).

    CRISPR:

    Article Title: High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
    Article Snippet: SRD5A3 KO hiPSCs clones were generated by CRISPR/Cas9. sgRNA (inserted into a GFP-containing PX458 plasmid, Addgene) targeting the first exon of the gene were generated via the CRISPOR website and validated in T293 HEK cells by Sanger sequencing combined with tides analysis ( https://tide-calculator.nki.nl/ ; data not shown). hiPSCs were transfected by nucleofection (Amaxa 4D, Lonza) and transfected cells (GFP+) were isolated by FACs (BD FACSAria II SORP, BD Biosciences) to generate single-cell-of-origin colonies. .. DNA was extracted from a piece of each colony by ZR-Duet DNA MiniPrep (D7003, Zymo) and sequenced.

    Mouse Assay:

    Article Title: Unexpected Cartilage Phenotype in CD4-Cre-Conditional SOS-Deficient Mice
    Article Snippet: Purification of CD4+ T Cells/DNA Isolation/Genomic PCR CD4+ T cells were isolated from lymph nodes and spleens of Sos1 f/f Sos2−/− CD4-Cre+ mice using EasySep Mouse CD4+ T Cell Isolation Kit (Stem Cell Technologies, Cambridge, MA, USA). .. Tissue DNA was isolated using DNA columns from a ZR-Duet DNA/RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA).

    Plasmid Preparation:

    Article Title: High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
    Article Snippet: SRD5A3 KO hiPSCs clones were generated by CRISPR/Cas9. sgRNA (inserted into a GFP-containing PX458 plasmid, Addgene) targeting the first exon of the gene were generated via the CRISPOR website and validated in T293 HEK cells by Sanger sequencing combined with tides analysis ( https://tide-calculator.nki.nl/ ; data not shown). hiPSCs were transfected by nucleofection (Amaxa 4D, Lonza) and transfected cells (GFP+) were isolated by FACs (BD FACSAria II SORP, BD Biosciences) to generate single-cell-of-origin colonies. .. DNA was extracted from a piece of each colony by ZR-Duet DNA MiniPrep (D7003, Zymo) and sequenced.

    RNA Extraction:

    Article Title: Discovery of a stem-like multipotent cell fate
    Article Snippet: .. All cells were directly sorted into DNA/RNA Shield Buffer from the Zymo Duet DNA/RNA MiniPrep Plus kit (Zymo #D7003), followed by RNA extraction as per provided protocol. .. RNA was submitted to the Johns Hopkins University Microarray Core for Human PrimeView Gene Expression Array (Affymetrix) analysis.

    Selection:

    Article Title: High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
    Article Snippet: DNA was extracted from a piece of each colony by ZR-Duet DNA MiniPrep (D7003, Zymo) and sequenced. .. After selection, SOX2 (1:2000; AB5603, Millipore) and OCT4 (1:100; SC5279, Santa Cruz) immunostaining was used to confirm pluripotency ( ).

    Sample Prep:

    Article Title: Genome-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer
    Article Snippet: 5 RNA sequencing (RNA-Seq) Total RNA from HCC1806 and MDA-MB-231 cells was extracted using ZR-Duet DNA/RNA MiniPrep Plus (cat# D7003; Zymo Research, Irvine, CA). .. RNA samples with high quality (RIN ≥ 8.0) and high purity (OD 260/280 = 1.8–2.0) scores were used to generate libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, CA).

    Homogenization:

    Article Title: SIRT1, miR-132 and miR-212 link human longevity to Alzheimer’s Disease
    Article Snippet: .. RNAs were extracted from these postmortem tissues following homogenization using Bullet Blender (Next Advance, Inc., NY, USA), and extraction with ZR-Duet DNA-RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA). ..

    Spectrophotometry:

    Article Title: Detection of Rickettsiae, Borreliae, and Ehrlichiae in Ticks Collected from Walker County, Texas, 2017–2018
    Article Snippet: DNA and RNA were co-extracted from half of the homogenate using the ZR Duet DNA/RNA MiniPrep Plus Kit (Zymo Research, Irvine, CA, USA), and the remaining homogenate was stored at −80 °C for further evaluation. .. The quality and quantity of DNA and RNA were analyzed by either NanoDrop 1000 or Denovix DS-11+ spectrophotometer prior to pathogen detection.

    Concentration Assay:

    Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
    Article Snippet: Brain lysate was placed on a sucrose solution (1.8 M sucrose, 3 mM Mg(Ac)2 , 10 mM Tris-HCl pH 8.0) to create a concentration gradient. .. After sorting, gDNA and total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit (#D7003, Zymo Research, Irvine, CA) according to the manufacturer’s instruction.

    Lysis:

    Article Title: Studying the microbiota of bats: Accuracy of direct and indirect samplings. Studying the microbiota of bats: Accuracy of direct and indirect samplings
    Article Snippet: .. 2.2 Sample processing DNA extraction was performed as detailed previously (Dietrich et al., ), using a ZR‐Duet DNA/RNA MiniPrep Plus kit (Zymo Research), and a pre‐treatment for robust lysis of Gram‐positive and Gram‐negative bacteria. .. We included three negative controls during DNA extraction to control for the presence of exogenous DNA in laboratory reagents and materials.

    Article Title: Cell type-specific epigenetic links to schizophrenia risk in the brain
    Article Snippet: Approximately 700 mg of frozen postmortem brain was homogenized with lysis buffer (0.32 M sucrose, 5 mM CaCl2 , 3 mM Mg(Ac)2 , 0.1 mM EDTA, 10 mM Tris-HCl pH 8.0, 0.1 mM PMSF, 0.1% (w/o) Triton X-100, 0.1% (w/o) NP-40, protease inhibitors (1:100) (#P8340, Sigma, St. Louis, MO), RNase inhibitors (1:200) (#AM2696, ThermoFisher, Waltham, MA)) using a Dounce homogenizer. .. After sorting, gDNA and total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit (#D7003, Zymo Research, Irvine, CA) according to the manufacturer’s instruction.

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    Zymo Research parallel dna rna extraction
    Microbial alignments detected in the lungs of immunocompromised children. Red dots represent potentially pathogenic microbes that are both abundant (≥10 rpm for bacteria or ≥1 rpm for fungi or viruses) and identified at levels greater than most other samples in the cohort (Z-score ≥2). Hollow red dots indicating Bocavirus and Pneumocystis are used to indicate organisms observed only once in this cohort. Blue dots represent all other potentially pathogenic microbes; light blue dots represent typically nonpathogenic microbes. Subplots show (A ) all bacteria, (B ) fungi, (C ) <t>RNA</t> viruses, and (D ) <t>DNA</t> viruses identified across all samples in the cohort. For the purpose of the Z-score calculation, the value of log 10 -transformed reads for undetected microbes was assumed to equal –2, just below the lower limit of detection for our sequencing depth (log 10 [0.01rpm] = –2). Abbreviation: seq, sequencing.
    Parallel Dna Rna Extraction, supplied by Zymo Research, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/parallel dna rna extraction/product/Zymo Research
    Average 95 stars, based on 1 article reviews
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    parallel dna rna extraction - by Bioz Stars, 2020-02
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    Zymo Research zr duet dna rna miniprep kit
    Identification of differentially abundant NOGs at the level of <t>DNA</t> 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, <t>RNA-seq</t> or both data sets (average across 16 samples). *Wilcoxon rank-sum test P
    Zr Duet Dna Rna Miniprep Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 95/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/zr duet dna rna miniprep kit/product/Zymo Research
    Average 95 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    zr duet dna rna miniprep kit - by Bioz Stars, 2020-02
    95/100 stars
      Buy from Supplier

    Image Search Results


    Microbial alignments detected in the lungs of immunocompromised children. Red dots represent potentially pathogenic microbes that are both abundant (≥10 rpm for bacteria or ≥1 rpm for fungi or viruses) and identified at levels greater than most other samples in the cohort (Z-score ≥2). Hollow red dots indicating Bocavirus and Pneumocystis are used to indicate organisms observed only once in this cohort. Blue dots represent all other potentially pathogenic microbes; light blue dots represent typically nonpathogenic microbes. Subplots show (A ) all bacteria, (B ) fungi, (C ) RNA viruses, and (D ) DNA viruses identified across all samples in the cohort. For the purpose of the Z-score calculation, the value of log 10 -transformed reads for undetected microbes was assumed to equal –2, just below the lower limit of detection for our sequencing depth (log 10 [0.01rpm] = –2). Abbreviation: seq, sequencing.

    Journal: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

    Article Title: Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

    doi: 10.1093/cid/ciy802

    Figure Lengend Snippet: Microbial alignments detected in the lungs of immunocompromised children. Red dots represent potentially pathogenic microbes that are both abundant (≥10 rpm for bacteria or ≥1 rpm for fungi or viruses) and identified at levels greater than most other samples in the cohort (Z-score ≥2). Hollow red dots indicating Bocavirus and Pneumocystis are used to indicate organisms observed only once in this cohort. Blue dots represent all other potentially pathogenic microbes; light blue dots represent typically nonpathogenic microbes. Subplots show (A ) all bacteria, (B ) fungi, (C ) RNA viruses, and (D ) DNA viruses identified across all samples in the cohort. For the purpose of the Z-score calculation, the value of log 10 -transformed reads for undetected microbes was assumed to equal –2, just below the lower limit of detection for our sequencing depth (log 10 [0.01rpm] = –2). Abbreviation: seq, sequencing.

    Article Snippet: Subsequently, all samples underwent 10 minutes of centrifugation at 4°C, and the supernatant was used for parallel DNA/RNA extraction (Zymo ZR-Duet DNA/RNA MiniPrep Kit).

    Techniques: Transformation Assay, Sequencing

    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

    Journal: The ISME Journal

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

    doi: 10.1038/ismej.2016.40

    Figure Lengend 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

    Article Snippet: Samples were centrifuged at 8000 g for 5 min and the supernatant was diluted with three volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep kit, Zymo Research).

    Techniques: 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

    Journal: The ISME Journal

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

    doi: 10.1038/ismej.2016.40

    Figure Lengend 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

    Article Snippet: Samples were centrifuged at 8000 g for 5 min and the supernatant was diluted with three volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep kit, Zymo Research).

    Techniques: DNA Sequencing, RNA Sequencing Assay

    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

    Journal: Nature Communications

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

    doi: 10.1038/s41467-017-01944-z

    Figure Lengend 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

    Article Snippet: Genomic DNA (gDNA) and RNA were isolated from male gWAT using ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research) of animals sacrificed at 33 weeks of age (after the diet challenge).

    Techniques: DNA Methylation Assay, Expressing, RNA Sequencing Assay

    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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0187636

    Figure Lengend 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.

    Article Snippet: DNA and RNA were then co-extracted from filters using the ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research, CA, USA), following the manufacturer’s protocol.

    Techniques:

    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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0187636

    Figure Lengend 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.

    Article Snippet: DNA and RNA were then co-extracted from filters using the ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research, CA, USA), following the manufacturer’s protocol.

    Techniques:

    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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0187636

    Figure Lengend 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.

    Article Snippet: DNA and RNA were then co-extracted from filters using the ZR-Duet™ DNA/RNA MiniPrep Kit (Zymo Research, CA, USA), following the manufacturer’s protocol.

    Techniques: