zr duet dna rna miniprep kit  (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
    Buy from Supplier


    Structured Review

    Zymo Research zr duet dna rna miniprep kit
    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/zr duet dna rna miniprep kit/product/Zymo Research
    Average 99 stars, based on 88 article reviews
    Price from $9.99 to $1999.99
    zr duet dna rna miniprep kit - by Bioz Stars, 2020-10
    99/100 stars

    Images

    1) 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

    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 "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:

    4) 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

    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 "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

    7) 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

    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 "Cell-type specific epigenetic links to schizophrenia risk in brain"

    Article Title: Cell-type specific epigenetic links to schizophrenia risk in brain

    Journal: bioRxiv

    doi: 10.1101/609131

    Gene expression signatures in NeuN + and OLIG2 + nuclei. a. Heatmap of cell-type DEGs with covariates indicated. b . Cell deconvolution of bulk RNA-seq data from the CommonMind Consortium and BrainSeq compared with NeuN + and OLIG2 + (control samples). Y-axes show the weighed proportion of cells that explain the expression of bulk RNA-seq c . Gene set enrichment for cell-type markers from single-nuclei RNA-seq. Enrichment analyses were performed using a Fisher’s Exact Test. Odds ratios and FDRs (within parentheses) are shown. d. Correspondence between expression change and methylation change in cell-types. The x-axis represents differential DNA methylation statistics for genes harboring DMRs in promoters. The y-axis indicates the log 2 (Fold Change) of expression between the two cell types. The negative correlation supports the well-established impact of promoter hypomethylation on upregulation of gene expression.
    Figure Legend Snippet: Gene expression signatures in NeuN + and OLIG2 + nuclei. a. Heatmap of cell-type DEGs with covariates indicated. b . Cell deconvolution of bulk RNA-seq data from the CommonMind Consortium and BrainSeq compared with NeuN + and OLIG2 + (control samples). Y-axes show the weighed proportion of cells that explain the expression of bulk RNA-seq c . Gene set enrichment for cell-type markers from single-nuclei RNA-seq. Enrichment analyses were performed using a Fisher’s Exact Test. Odds ratios and FDRs (within parentheses) are shown. d. Correspondence between expression change and methylation change in cell-types. The x-axis represents differential DNA methylation statistics for genes harboring DMRs in promoters. The y-axis indicates the log 2 (Fold Change) of expression between the two cell types. The negative correlation supports the well-established impact of promoter hypomethylation on upregulation of gene expression.

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

    Experimental design and FANS workflow example. a. Post-mortem brain tissue from BA46 was matched between cases with schizophrenia and unaffected individuals. Tissue pieces were processed to isolate nuclei and incubated with antibodies directed towards NeuN or OLIG2. The nuclei were sorted using fluorescence-activated nuclei sorting (FANS) to obtain purified populations of cell-types. Nuclei were processed to obtain genomic DNA (gDNA) and nuclear RNA from the same pools. Nucleic acids then underwent whole-genome sequencing (WGS), whole-genome bisulfite sequencing (WGBS), or RNA-sequencing (RNA-seq). b. NeuN-positive (NeuN + ) nuclei represent neurons within the cerebral cortex as few human NeuN-negative (NeuN − ) cells in the cortex are neurons 30 , 31 (e.g. Cajal-Retzius neurons). OLIG2-positive (OLIG2 + ) nuclei represent oligodendrocytes and their precursors 32 , 33 . Isolation of nuclei expressing either NeuN conjugated to Alexa 488 or OLIG2 conjugated to Alexa 555. Nuclei were first sorted for size and complexity, followed by gating to exclude doublets that indicate aggregates of nuclei, and then further sorted to isolate nuclei based on fluorescence. “Neg” nuclei are those that are neither NeuN + nor OLIG2 + . c. Example percentage nuclei at each selection step during FANS. Note that while in this example more nuclei were OLIG2 + , in other samples, the proportions might be reversed. d. Immunocytochemistry of nuclei post-sorting. Nuclei express either NeuN or OLIG2 or are negative for both after FANS. DAPI labels all nuclei.
    Figure Legend Snippet: Experimental design and FANS workflow example. a. Post-mortem brain tissue from BA46 was matched between cases with schizophrenia and unaffected individuals. Tissue pieces were processed to isolate nuclei and incubated with antibodies directed towards NeuN or OLIG2. The nuclei were sorted using fluorescence-activated nuclei sorting (FANS) to obtain purified populations of cell-types. Nuclei were processed to obtain genomic DNA (gDNA) and nuclear RNA from the same pools. Nucleic acids then underwent whole-genome sequencing (WGS), whole-genome bisulfite sequencing (WGBS), or RNA-sequencing (RNA-seq). b. NeuN-positive (NeuN + ) nuclei represent neurons within the cerebral cortex as few human NeuN-negative (NeuN − ) cells in the cortex are neurons 30 , 31 (e.g. Cajal-Retzius neurons). OLIG2-positive (OLIG2 + ) nuclei represent oligodendrocytes and their precursors 32 , 33 . Isolation of nuclei expressing either NeuN conjugated to Alexa 488 or OLIG2 conjugated to Alexa 555. Nuclei were first sorted for size and complexity, followed by gating to exclude doublets that indicate aggregates of nuclei, and then further sorted to isolate nuclei based on fluorescence. “Neg” nuclei are those that are neither NeuN + nor OLIG2 + . c. Example percentage nuclei at each selection step during FANS. Note that while in this example more nuclei were OLIG2 + , in other samples, the proportions might be reversed. d. Immunocytochemistry of nuclei post-sorting. Nuclei express either NeuN or OLIG2 or are negative for both after FANS. DAPI labels all nuclei.

    Techniques Used: Incubation, Fluorescence, Purification, Sequencing, Methylation Sequencing, RNA Sequencing Assay, Isolation, Expressing, Selection, Immunocytochemistry

    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 "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

    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 "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

    16) 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:

    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) 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

    18) Product Images from "Epigenetic regulation of hematopoiesis by DNA methylation"

    Article Title: Epigenetic regulation of hematopoiesis by DNA methylation

    Journal: eLife

    doi: 10.7554/eLife.11813

    Analysisof RNA seq and DNA methylation. ( a ) Schematic diagram depicting the workflow for global RNAseq and DNA methylation (RRBS) analysis of control or dnmt3bb.1 deficient HSPCs. ( b ) RNA seq analysis showing upregulation of cell death genes in dnmt3bb.1-deficient HSPCs. ( c,d ) Bisulfite sequencing of CpG islands from hematopoietic (c) and endothelial (d) genes identified in the RNAseq analysis including hematopoietic genes gata3, lmo2, erg, bmp4 and runx1 , c, and endothelial genes dll4, etv2, cldn5b and cdh5 , d. None of the genes showed changes in methylation of their CpG islands. DOI: http://dx.doi.org/10.7554/eLife.11813.011
    Figure Legend Snippet: Analysisof RNA seq and DNA methylation. ( a ) Schematic diagram depicting the workflow for global RNAseq and DNA methylation (RRBS) analysis of control or dnmt3bb.1 deficient HSPCs. ( b ) RNA seq analysis showing upregulation of cell death genes in dnmt3bb.1-deficient HSPCs. ( c,d ) Bisulfite sequencing of CpG islands from hematopoietic (c) and endothelial (d) genes identified in the RNAseq analysis including hematopoietic genes gata3, lmo2, erg, bmp4 and runx1 , c, and endothelial genes dll4, etv2, cldn5b and cdh5 , d. None of the genes showed changes in methylation of their CpG islands. DOI: http://dx.doi.org/10.7554/eLife.11813.011

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

    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

    Related Articles

    Real-time Polymerase Chain Reaction:

    Article Title: Follicular Helper T Cells Are Major Human Immunodeficiency Virus-2 Reservoirs and Support Productive Infection
    Article Snippet: .. Quantification of Cell-Associated Human Immunodeficiency Virus Deoxyribonucleic Acid and gag Messenger Ribonucleic Acid by Real-Time Polymerase Chain Reaction Total DNA and RNA were extracted from cell pellets of in vitro-infected Tfh and sort-purified blood CD4 T-cell subsets, using AllPrep DNA/RNA Micro kit (QIAGEN) and ZR-Duet DNA/RNA MiniPrep kit (Zymo Research), respectively. .. For gag messenger RNA (mRNA) quantification, 80 ng of total RNA was used to synthesize complementary DNA using oligo(dT)20 and SuperScript III RT (Invitrogen).

    Isolation:

    Article Title: An epigenetic mechanism for cavefish eye degeneration
    Article Snippet: .. RNA isolation and sequencing Total cellular RNA and DNA was isolated from the harvested eyes using ZR Duet DNA/RNA miniprep kit (Zymo Research). .. 300-900ng poly-A enriched RNA was converted to indexed sequencing libraries using the TruSeq Standard mRNA library prep kit (Illumina).

    Article Title: Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice
    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). .. Nucleic acid samples from 4 randomly selected mice from control or TBT groups were submitted for DNA methylome and transcriptome analyses.

    Sequencing:

    Article Title: An epigenetic mechanism for cavefish eye degeneration
    Article Snippet: .. RNA isolation and sequencing Total cellular RNA and DNA was isolated from the harvested eyes using ZR Duet DNA/RNA miniprep kit (Zymo Research). .. 300-900ng poly-A enriched RNA was converted to indexed sequencing libraries using the TruSeq Standard mRNA library prep kit (Illumina).

    Purification:

    Article Title: Cell-type specific epigenetic links to schizophrenia risk in 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. ..

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    Zymo Research zr duet dna rna miniprep kit
    Ancestral TBT exposure leads to altered <t>DNA</t> 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 <t>RNA-seq</t> 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
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    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

    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

    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:

    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

    Journal: Nature ecology & evolution

    Article Title: An epigenetic mechanism for cavefish eye degeneration

    doi: 10.1038/s41559-018-0569-4

    Figure Lengend 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

    Article Snippet: RNA isolation and sequencing Total cellular RNA and DNA was isolated from the harvested eyes using ZR Duet DNA/RNA miniprep kit (Zymo Research).

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