methylc seq libraries  (Qiagen)

 
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    DNeasy Plant Mini Kit
    Description:
    For isolation of up to 30 µg total cellular DNA from plant cells and tissues or fungi Kit contents Qiagen DNeasy Plant Mini Kit 50 preps 100mg Sample 50 to 400L Elution Volume Plant Cells Tissues Sample DNA Purification Silica Technology Spin Column Format 3 to 30g Yield Rapid Isolation of Ready to use DNA For Isolation of up to 30g Total Cellular DNA from Plant Cells Tissues or Fungi Includes 50 DNeasy Mini Spin Columns 50 QIAshredder Mini Spin Columns RNase A Buffers 2mL Collection Tubes Benefits Pure DNA free from contaminants and enzyme inhibitors Rapid isolation of ready to use DNA No organic extraction no ethanol precipitatio
    Catalog Number:
    69104
    Price:
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    DNeasy Plant Mini Kit
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    Structured Review

    Qiagen methylc seq libraries
    DNeasy Plant Mini Kit
    For isolation of up to 30 µg total cellular DNA from plant cells and tissues or fungi Kit contents Qiagen DNeasy Plant Mini Kit 50 preps 100mg Sample 50 to 400L Elution Volume Plant Cells Tissues Sample DNA Purification Silica Technology Spin Column Format 3 to 30g Yield Rapid Isolation of Ready to use DNA For Isolation of up to 30g Total Cellular DNA from Plant Cells Tissues or Fungi Includes 50 DNeasy Mini Spin Columns 50 QIAshredder Mini Spin Columns RNase A Buffers 2mL Collection Tubes Benefits Pure DNA free from contaminants and enzyme inhibitors Rapid isolation of ready to use DNA No organic extraction no ethanol precipitatio
    https://www.bioz.com/result/methylc seq libraries/product/Qiagen
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    methylc seq libraries - by Bioz Stars, 2020-09
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    Images

    1) Product Images from "SUVH1, a Su(var)3–9 family member, promotes the expression of genes targeted by DNA methylation"

    Article Title: SUVH1, a Su(var)3–9 family member, promotes the expression of genes targeted by DNA methylation

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv958

    The suvh1–1 mutation does not affect DNA methylation. ( A and B ) McrBC-qPCR analysis of DNA methylation levels at the d35S promoter and the LUC coding region in YJ (A) and LUCH (B). qPCR was performed using genomic DNA treated with or without McrBC. The relative levels of amplified DNA for UBQ5, LUC and d35S in samples treated with McrBC compared to untreated samples were shown. Error bars were from three technical replicates. Two biological replicates were performed and gave similar results. ( C and D ) The levels of CG, CHG and CHH DNA methylation at the d35S promoter (C) and LUC coding region (D) in YJ and YJ suvh1–1 as determined through MethylC sequencing. Results from two biological replicates (rep) are shown. (E) Total genomic CG, CHG and CHH DNA methylation in YJ and YJ suvh1–1 as determined through MethylC-seq. Results from two biological replicates (rep) are shown.
    Figure Legend Snippet: The suvh1–1 mutation does not affect DNA methylation. ( A and B ) McrBC-qPCR analysis of DNA methylation levels at the d35S promoter and the LUC coding region in YJ (A) and LUCH (B). qPCR was performed using genomic DNA treated with or without McrBC. The relative levels of amplified DNA for UBQ5, LUC and d35S in samples treated with McrBC compared to untreated samples were shown. Error bars were from three technical replicates. Two biological replicates were performed and gave similar results. ( C and D ) The levels of CG, CHG and CHH DNA methylation at the d35S promoter (C) and LUC coding region (D) in YJ and YJ suvh1–1 as determined through MethylC sequencing. Results from two biological replicates (rep) are shown. (E) Total genomic CG, CHG and CHH DNA methylation in YJ and YJ suvh1–1 as determined through MethylC-seq. Results from two biological replicates (rep) are shown.

    Techniques Used: Mutagenesis, DNA Methylation Assay, Real-time Polymerase Chain Reaction, Amplification, Sequencing

    Plots of DNA methylation levels at 1 kb gene promoter regions versus gene expression levels in YJ and YJ suvh1–1 . The x-axis represents the level of DNA methylation, and the y-axis represents the natural logarithm of the RPKM (reads per kilobase per million) value for genes from mRNA-seq. ( A and B ) Correlation plot of CG methylation level with gene expression in YJ (A) and YJ suvh1–1 (B). ( C and D ) Correlation plot of CHG methylation level with gene expression in YJ (C) and YJ suvh1–1 (D). ( E and F ) Correlation plot of CHH methylation level with gene expression in YJ (E) and YJ suvh1–1 (F) DNA methylation and gene expression levels were determined from MethylC-seq and mRNA-seq, respectively, in this study.
    Figure Legend Snippet: Plots of DNA methylation levels at 1 kb gene promoter regions versus gene expression levels in YJ and YJ suvh1–1 . The x-axis represents the level of DNA methylation, and the y-axis represents the natural logarithm of the RPKM (reads per kilobase per million) value for genes from mRNA-seq. ( A and B ) Correlation plot of CG methylation level with gene expression in YJ (A) and YJ suvh1–1 (B). ( C and D ) Correlation plot of CHG methylation level with gene expression in YJ (C) and YJ suvh1–1 (D). ( E and F ) Correlation plot of CHH methylation level with gene expression in YJ (E) and YJ suvh1–1 (F) DNA methylation and gene expression levels were determined from MethylC-seq and mRNA-seq, respectively, in this study.

    Techniques Used: DNA Methylation Assay, Expressing, Methylation

    2) Product Images from "SUVH1, a Su(var)3–9 family member, promotes the expression of genes targeted by DNA methylation"

    Article Title: SUVH1, a Su(var)3–9 family member, promotes the expression of genes targeted by DNA methylation

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv958

    The suvh1–1 mutation does not affect DNA methylation. ( A and B ) McrBC-qPCR analysis of DNA methylation levels at the d35S promoter and the LUC coding region in YJ (A) and LUCH (B). qPCR was performed using genomic DNA treated with or without McrBC. The relative levels of amplified DNA for UBQ5, LUC and d35S in samples treated with McrBC compared to untreated samples were shown. Error bars were from three technical replicates. Two biological replicates were performed and gave similar results. ( C and D ) The levels of CG, CHG and CHH DNA methylation at the d35S promoter (C) and LUC coding region (D) in YJ and YJ suvh1–1 as determined through MethylC sequencing. Results from two biological replicates (rep) are shown. (E) Total genomic CG, CHG and CHH DNA methylation in YJ and YJ suvh1–1 as determined through MethylC-seq. Results from two biological replicates (rep) are shown.
    Figure Legend Snippet: The suvh1–1 mutation does not affect DNA methylation. ( A and B ) McrBC-qPCR analysis of DNA methylation levels at the d35S promoter and the LUC coding region in YJ (A) and LUCH (B). qPCR was performed using genomic DNA treated with or without McrBC. The relative levels of amplified DNA for UBQ5, LUC and d35S in samples treated with McrBC compared to untreated samples were shown. Error bars were from three technical replicates. Two biological replicates were performed and gave similar results. ( C and D ) The levels of CG, CHG and CHH DNA methylation at the d35S promoter (C) and LUC coding region (D) in YJ and YJ suvh1–1 as determined through MethylC sequencing. Results from two biological replicates (rep) are shown. (E) Total genomic CG, CHG and CHH DNA methylation in YJ and YJ suvh1–1 as determined through MethylC-seq. Results from two biological replicates (rep) are shown.

    Techniques Used: Mutagenesis, DNA Methylation Assay, Real-time Polymerase Chain Reaction, Amplification, Sequencing

    Plots of DNA methylation levels at 1 kb gene promoter regions versus gene expression levels in YJ and YJ suvh1–1 . The x-axis represents the level of DNA methylation, and the y-axis represents the natural logarithm of the RPKM (reads per kilobase per million) value for genes from mRNA-seq. ( A and B ) Correlation plot of CG methylation level with gene expression in YJ (A) and YJ suvh1–1 (B). ( C and D ) Correlation plot of CHG methylation level with gene expression in YJ (C) and YJ suvh1–1 (D). ( E and F ) Correlation plot of CHH methylation level with gene expression in YJ (E) and YJ suvh1–1 (F) DNA methylation and gene expression levels were determined from MethylC-seq and mRNA-seq, respectively, in this study.
    Figure Legend Snippet: Plots of DNA methylation levels at 1 kb gene promoter regions versus gene expression levels in YJ and YJ suvh1–1 . The x-axis represents the level of DNA methylation, and the y-axis represents the natural logarithm of the RPKM (reads per kilobase per million) value for genes from mRNA-seq. ( A and B ) Correlation plot of CG methylation level with gene expression in YJ (A) and YJ suvh1–1 (B). ( C and D ) Correlation plot of CHG methylation level with gene expression in YJ (C) and YJ suvh1–1 (D). ( E and F ) Correlation plot of CHH methylation level with gene expression in YJ (E) and YJ suvh1–1 (F) DNA methylation and gene expression levels were determined from MethylC-seq and mRNA-seq, respectively, in this study.

    Techniques Used: DNA Methylation Assay, Expressing, Methylation

    3) Product Images from "Nickel and low CO2-controlled motility in Chlamydomonas through complementation of a paralyzed flagella mutant with chemically regulated promoters"

    Article Title: Nickel and low CO2-controlled motility in Chlamydomonas through complementation of a paralyzed flagella mutant with chemically regulated promoters

    Journal: BMC Plant Biology

    doi: 10.1186/1471-2229-11-22

    Western blot of CYC6:RSP3-HA and CAH1:RSP3-HA transformants, probed with the anti-HA antibody . Panels A and B: Screening of protein extracts CYC6:RSP3-HA and CAH1:RSP3-HA transformants, extracted, respectively, 48 h and 6 h after induction. Transformants that exhibit inducible swimming are labeled. Arrows point at the RPS3-HA bands. Cultures were grown and induced as in Figures 3 and 4, extracted, and 20 μg total proteins were loaded on each lane. Panel C: Re-analysis of transformants exhibiting inducible swimming (from Panels A and B). Cultures were grown and induced as in Figure 6, extracted, and 40 μg total proteins were loaded on each lane. For details, see Methods.
    Figure Legend Snippet: Western blot of CYC6:RSP3-HA and CAH1:RSP3-HA transformants, probed with the anti-HA antibody . Panels A and B: Screening of protein extracts CYC6:RSP3-HA and CAH1:RSP3-HA transformants, extracted, respectively, 48 h and 6 h after induction. Transformants that exhibit inducible swimming are labeled. Arrows point at the RPS3-HA bands. Cultures were grown and induced as in Figures 3 and 4, extracted, and 20 μg total proteins were loaded on each lane. Panel C: Re-analysis of transformants exhibiting inducible swimming (from Panels A and B). Cultures were grown and induced as in Figure 6, extracted, and 40 μg total proteins were loaded on each lane. For details, see Methods.

    Techniques Used: Western Blot, Labeling

    Chemically inducible complementation of the pf14 mutant by the CYC6:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 48 hours after Ni addition. The transformants were grown in TAP ENEA2 medium in 24-well microtiter plates and induced at mid-log phase with 25 μM Ni. For details, see Methods.
    Figure Legend Snippet: Chemically inducible complementation of the pf14 mutant by the CYC6:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 48 hours after Ni addition. The transformants were grown in TAP ENEA2 medium in 24-well microtiter plates and induced at mid-log phase with 25 μM Ni. For details, see Methods.

    Techniques Used: Mutagenesis, Construct

    Chemically inducible complementation of the pf14 mutant by the CAH1:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 6 hours after induction by low CO 2 . The transformants were grown in minimal medium with extra phosphate in 24-well microtiter plates, under air containing 5% CO 2 , and induced at early log phase by shifting to air with no CO 2 supplementation. For details, see Methods.
    Figure Legend Snippet: Chemically inducible complementation of the pf14 mutant by the CAH1:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 6 hours after induction by low CO 2 . The transformants were grown in minimal medium with extra phosphate in 24-well microtiter plates, under air containing 5% CO 2 , and induced at early log phase by shifting to air with no CO 2 supplementation. For details, see Methods.

    Techniques Used: Mutagenesis, Construct

    Time course of inducible swimming in one CYC6:RSP3-HA (Panel A) and one CAH1:RSP3-HA (Panel B) transformant . The CYC6:RSP3-HA transformant was grown in 6 ml in 6-well microtiter plates with shaking (120 rpm) and the CAH1:RSP3-HA transformant was grown in 150 ml in 250-ml Erlenmeyer flasks with bubbling.
    Figure Legend Snippet: Time course of inducible swimming in one CYC6:RSP3-HA (Panel A) and one CAH1:RSP3-HA (Panel B) transformant . The CYC6:RSP3-HA transformant was grown in 6 ml in 6-well microtiter plates with shaking (120 rpm) and the CAH1:RSP3-HA transformant was grown in 150 ml in 250-ml Erlenmeyer flasks with bubbling.

    Techniques Used:

    4) Product Images from "Promoting the accumulation of scopolamine and hyoscyamine in Hyoscyamus niger L. through EMS based mutagenesis"

    Article Title: Promoting the accumulation of scopolamine and hyoscyamine in Hyoscyamus niger L. through EMS based mutagenesis

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0231355

    Representative image of DNA extraction and PCR analysis of H6H and PMT gene isolated from EMS treated and control explants of H . niger of different samples (500 and 400bp respectively) of (A) DNA extraction isolated from explants treated with different concentrations of EMS and untreated. (B) Depicts the PCR analysis of H6H (500bp) Gene (C) PCR amplification PMT Gene (400bp).
    Figure Legend Snippet: Representative image of DNA extraction and PCR analysis of H6H and PMT gene isolated from EMS treated and control explants of H . niger of different samples (500 and 400bp respectively) of (A) DNA extraction isolated from explants treated with different concentrations of EMS and untreated. (B) Depicts the PCR analysis of H6H (500bp) Gene (C) PCR amplification PMT Gene (400bp).

    Techniques Used: DNA Extraction, Polymerase Chain Reaction, Isolation, Amplification

    5) Product Images from "Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species"

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species

    Journal:

    doi:

    Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;
    Figure Legend Snippet: Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;

    Techniques Used: DNA Extraction, Infection, Polymerase Chain Reaction

    6) Product Images from "Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species"

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species

    Journal:

    doi:

    Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;
    Figure Legend Snippet: Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;

    Techniques Used: DNA Extraction, Infection, Polymerase Chain Reaction

    7) Product Images from "In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes"

    Article Title: In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes

    Journal: Plants

    doi: 10.3390/plants6040052

    Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.
    Figure Legend Snippet: Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.

    Techniques Used: DNA Extraction, Modification

    Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.
    Figure Legend Snippet: Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.

    Techniques Used: DNA Extraction, Modification

    8) Product Images from "A reference-grade wild soybean genome"

    Article Title: A reference-grade wild soybean genome

    Journal: Nature Communications

    doi: 10.1038/s41467-019-09142-9

    Causal structural variation that controls soybean seed coat pigmentation. a Sequence comparison between W05 genome and Wm82 bacterial artificial chromosome (BAC) sequences at the I locus region. CHS genes and subtilisin gene/gene fragments are indicated with blue and orange, respectively. b Top panel: cartoon shows the exon structure of the subtilisin gene fragment (orange), the CHS1 gene (blue), and the Expressed Sequence Tag (EST) sequence Gm-c1069–6017. Positions of primers designed for PCR amplification of subtilisin-anti- CHS1 chimeric transcript are indicated with black arrows. Bottom panel: PCR amplification of the subtilisin-anti- CHS1 chimeric transcript. Experiment was repeated at least twice with independent samples. Marker: 1 Kb Plus DNA ladder (NEB, cat. N3200S). NTC, no template control. GmACT11 is used as a housekeeping control. Unprocessed gel image is provided in Source Data file. c Proposed model for the generation of siRNAs originated from a large structural rearrangement in the I locus. CHS genes and the subtilisin gene/gene fragments are illustrated as blue and orange, respectively. Arrowheads indicated the direction of transcription that causes the formation of double-stranded RNA. Cluster A and B are named according to a previous report 23 . IR-CHS gene cluster: inverted repeat of CHS gene cluster
    Figure Legend Snippet: Causal structural variation that controls soybean seed coat pigmentation. a Sequence comparison between W05 genome and Wm82 bacterial artificial chromosome (BAC) sequences at the I locus region. CHS genes and subtilisin gene/gene fragments are indicated with blue and orange, respectively. b Top panel: cartoon shows the exon structure of the subtilisin gene fragment (orange), the CHS1 gene (blue), and the Expressed Sequence Tag (EST) sequence Gm-c1069–6017. Positions of primers designed for PCR amplification of subtilisin-anti- CHS1 chimeric transcript are indicated with black arrows. Bottom panel: PCR amplification of the subtilisin-anti- CHS1 chimeric transcript. Experiment was repeated at least twice with independent samples. Marker: 1 Kb Plus DNA ladder (NEB, cat. N3200S). NTC, no template control. GmACT11 is used as a housekeeping control. Unprocessed gel image is provided in Source Data file. c Proposed model for the generation of siRNAs originated from a large structural rearrangement in the I locus. CHS genes and the subtilisin gene/gene fragments are illustrated as blue and orange, respectively. Arrowheads indicated the direction of transcription that causes the formation of double-stranded RNA. Cluster A and B are named according to a previous report 23 . IR-CHS gene cluster: inverted repeat of CHS gene cluster

    Techniques Used: Sequencing, BAC Assay, Polymerase Chain Reaction, Amplification, Marker

    Large structural variations in soybean genomes detected by OM. a Seed coat pigmentation causal inversion in the I locus. Pink regions are the aligned flanking regions of the I locus. Aligned blocks in the I locus are painted in different colors to illustrate the inversion and duplication in accessions with colorless seed coat. b Reciprocal inter-chromosomal translocation between chromosomes 11 and 13. Segments in blue and red are regions homologous to the W05 chromosomes 11 and 13, respectively. Segments in gray contains optical signals that cannot be aligned to the W05 in silico map. c A previously reported cultivated soybean-specific region on chromosome 15 7 . Blue regions are the aligned flanking region of the previously proposed cultivated soybean-specific region. Segments that cannot be aligned with W05 in silico map are shown in gray. d Length polymorphism of a KTI gene cluster in chromosome 8. Orange triangles indicate the location of KTI genes in W05 (top track) and Wm82_v2 (bottom track), respectively. KTI , Kunitz trypsin inhibitor genes. Asterisks (*) next to the accession IDs indicate the use of in silico map instead of optical contigs
    Figure Legend Snippet: Large structural variations in soybean genomes detected by OM. a Seed coat pigmentation causal inversion in the I locus. Pink regions are the aligned flanking regions of the I locus. Aligned blocks in the I locus are painted in different colors to illustrate the inversion and duplication in accessions with colorless seed coat. b Reciprocal inter-chromosomal translocation between chromosomes 11 and 13. Segments in blue and red are regions homologous to the W05 chromosomes 11 and 13, respectively. Segments in gray contains optical signals that cannot be aligned to the W05 in silico map. c A previously reported cultivated soybean-specific region on chromosome 15 7 . Blue regions are the aligned flanking region of the previously proposed cultivated soybean-specific region. Segments that cannot be aligned with W05 in silico map are shown in gray. d Length polymorphism of a KTI gene cluster in chromosome 8. Orange triangles indicate the location of KTI genes in W05 (top track) and Wm82_v2 (bottom track), respectively. KTI , Kunitz trypsin inhibitor genes. Asterisks (*) next to the accession IDs indicate the use of in silico map instead of optical contigs

    Techniques Used: Translocation Assay, In Silico

    Distribution of W05 genomic features. The outer layer illustrates the 20 chromosomes of W05 in megabases (Mb). a Repeat coverage was calculated by the occupancy of repeat sequence in 1 Mb window (step size: 500 Kb). b Gene coverage was calculated by the occupancy of coding sequence in 1 Mb window (step size: 500 Kb). c GC content was calculated in a 200 Kb window. d Position of simple sequence repeat (SSR) markers were indicated in purple. Marker information could be found in Supplementary Data 1 . e Presence of telomeric tandem arrays and cent91/92 soybean specific type centromeric repeats were marked in pink and blue, respectively
    Figure Legend Snippet: Distribution of W05 genomic features. The outer layer illustrates the 20 chromosomes of W05 in megabases (Mb). a Repeat coverage was calculated by the occupancy of repeat sequence in 1 Mb window (step size: 500 Kb). b Gene coverage was calculated by the occupancy of coding sequence in 1 Mb window (step size: 500 Kb). c GC content was calculated in a 200 Kb window. d Position of simple sequence repeat (SSR) markers were indicated in purple. Marker information could be found in Supplementary Data 1 . e Presence of telomeric tandem arrays and cent91/92 soybean specific type centromeric repeats were marked in pink and blue, respectively

    Techniques Used: Sequencing, Marker

    9) Product Images from "The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing"

    Article Title: The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing

    Journal: The EMBO Journal

    doi: 10.15252/embj.201798770

    Analysis of enhancer of polycomb‐like proteins in Arabidopsis
    Figure Legend Snippet: Analysis of enhancer of polycomb‐like proteins in Arabidopsis

    Techniques Used:

    10) Product Images from "Group III-A XTH Genes of Arabidopsis Encode Predominant Xyloglucan Endohydrolases That Are Dispensable for Normal Growth"

    Article Title: Group III-A XTH Genes of Arabidopsis Encode Predominant Xyloglucan Endohydrolases That Are Dispensable for Normal Growth

    Journal: Plant Physiology

    doi: 10.1104/pp.112.207308

    . B, xth31-1 / xth32-1 double knockout. C, A second example of xth31-1 / xth32-1 double knockout. Numbered zones show the approximate positions at which
    Figure Legend Snippet: . B, xth31-1 / xth32-1 double knockout. C, A second example of xth31-1 / xth32-1 double knockout. Numbered zones show the approximate positions at which

    Techniques Used: Double Knockout

    , the region corresponding to the top portion of (approximately 2 mm from the root tip). B, xth31-1 / xth32-1 double knockout, the region
    Figure Legend Snippet: , the region corresponding to the top portion of (approximately 2 mm from the root tip). B, xth31-1 / xth32-1 double knockout, the region

    Techniques Used: Double Knockout

    . The inset (arrow) with detector attenuation highlights root hair initiation and root hair staining. B, xth31-1 / xth32-1 double knockout, showing root hair initiation
    Figure Legend Snippet: . The inset (arrow) with detector attenuation highlights root hair initiation and root hair staining. B, xth31-1 / xth32-1 double knockout, showing root hair initiation

    Techniques Used: Staining, Double Knockout

    . C and D, Confocal fluorescence (C) and bright-field (D) images of xth31-1 / xth32-1 double knockout.
    Figure Legend Snippet: . C and D, Confocal fluorescence (C) and bright-field (D) images of xth31-1 / xth32-1 double knockout.

    Techniques Used: Fluorescence, Double Knockout

    11) Product Images from "Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W]Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W] [OA]"

    Article Title: Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W]Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W] [OA]

    Journal: Plant Physiology

    doi: 10.1104/pp.110.169045

    TOR kinase domain is essential for embryo development in Arabidopsis. A, A series of T-DNA insertion mutants from N to C terminal of TOR were genotyped and phenotyped. tor - 3 (SALK_036379), tor - 4 (SALK_007654), tor - 5 (SALK_147473), tor - 6 (SALK_017177),
    Figure Legend Snippet: TOR kinase domain is essential for embryo development in Arabidopsis. A, A series of T-DNA insertion mutants from N to C terminal of TOR were genotyped and phenotyped. tor - 3 (SALK_036379), tor - 4 (SALK_007654), tor - 5 (SALK_147473), tor - 6 (SALK_017177),

    Techniques Used:

    TOR interacts with the promoter and 5′-ETS of the ribosome RNA gene and regulates ribosome rRNA expression in Arabidopsis. A, The organization of the 45S rRNA gene in Arabidopsis and the location of 18 overlapping PCR fragments spanning 45S rRNA
    Figure Legend Snippet: TOR interacts with the promoter and 5′-ETS of the ribosome RNA gene and regulates ribosome rRNA expression in Arabidopsis. A, The organization of the 45S rRNA gene in Arabidopsis and the location of 18 overlapping PCR fragments spanning 45S rRNA

    Techniques Used: Expressing, Polymerase Chain Reaction

    12) Product Images from "A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis"

    Article Title: A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2015.00048

    The quantitative analyses of transcripts, extrachromosomal DNAs, and newly transposed copies in progeny. WT and nrpd1 plants were exposed to HS for 6 h and for 24 h at 7 days after germination. NS, non-stressed samples. (A) Relative transcription level of ONSEN . Error bar represents the mean ± SEM, n = 3, values relative to 24 h heat-stressed WT. (B) Relative number of copies of extrachromosomal DNA of ONSEN . Error bar represents the mean ± SEM, n = 3; values are relative to the NS WT seedlings. (C) Southern blot analysis of ONSEN in progeny plants.
    Figure Legend Snippet: The quantitative analyses of transcripts, extrachromosomal DNAs, and newly transposed copies in progeny. WT and nrpd1 plants were exposed to HS for 6 h and for 24 h at 7 days after germination. NS, non-stressed samples. (A) Relative transcription level of ONSEN . Error bar represents the mean ± SEM, n = 3, values relative to 24 h heat-stressed WT. (B) Relative number of copies of extrachromosomal DNA of ONSEN . Error bar represents the mean ± SEM, n = 3; values are relative to the NS WT seedlings. (C) Southern blot analysis of ONSEN in progeny plants.

    Techniques Used: Southern Blot

    Structure of the gene construct used to produce transgenic plants, and the insertion position of the transgene in the genome. (A) The structure of the DNA sequence between the left border (LB) and the right border (RB) of the T-DNA. Intact long terminal repeat (LTR) of ONSEN ( AT5G13205 ) was fused with the green fluorescent protein ( GFP ) gene. (B) The transgene was inserted in the intergenic region between At1g26850 and At1g26860 , in the same direction. Numerals indicate the nucleotide number according to the AGI map.
    Figure Legend Snippet: Structure of the gene construct used to produce transgenic plants, and the insertion position of the transgene in the genome. (A) The structure of the DNA sequence between the left border (LB) and the right border (RB) of the T-DNA. Intact long terminal repeat (LTR) of ONSEN ( AT5G13205 ) was fused with the green fluorescent protein ( GFP ) gene. (B) The transgene was inserted in the intergenic region between At1g26850 and At1g26860 , in the same direction. Numerals indicate the nucleotide number according to the AGI map.

    Techniques Used: Construct, Transgenic Assay, Sequencing

    13) Product Images from "Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W]Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W] [OA]"

    Article Title: Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W]Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W] [OA]

    Journal: Plant Physiology

    doi: 10.1104/pp.110.169045

    TOR kinase domain is essential for embryo development in Arabidopsis. A, A series of T-DNA insertion mutants from N to C terminal of TOR were genotyped and phenotyped. tor - 3 (SALK_036379), tor - 4 (SALK_007654), tor - 5 (SALK_147473), tor - 6 (SALK_017177),
    Figure Legend Snippet: TOR kinase domain is essential for embryo development in Arabidopsis. A, A series of T-DNA insertion mutants from N to C terminal of TOR were genotyped and phenotyped. tor - 3 (SALK_036379), tor - 4 (SALK_007654), tor - 5 (SALK_147473), tor - 6 (SALK_017177),

    Techniques Used:

    14) Product Images from "METHIONINE ADENOSYLTRANSFERASE4 Mediates DNA and Histone Methylation 1METHIONINE ADENOSYLTRANSFERASE4 Mediates DNA and Histone Methylation 1 [OPEN]"

    Article Title: METHIONINE ADENOSYLTRANSFERASE4 Mediates DNA and Histone Methylation 1METHIONINE ADENOSYLTRANSFERASE4 Mediates DNA and Histone Methylation 1 [OPEN]

    Journal: Plant Physiology

    doi: 10.1104/pp.18.00183

    MAT4 interacts with different MATs in plants. A, MAT4 interacted with MAT1, MAT2, MAT3, or MAT4 itself in a protein co-IP assay. Total proteins were extracted from Arabidopsis protoplasts transiently coexpressing the MAT4-FLAG with MAT1-, MAT2-, MAT3-, MAT4-GFP, or GFP (as a negative control) plasmids and immunoprecipitated with anti-GFP beads. The co-IP proteins were immunoblotted with anti-FLAG and anti-GFP antibodies. B, Protein pull-down assay for MAT4 interaction with MAT1, MAT2, MAT3, or MAT4 itself. Total proteins were isolated from E. coli coexpressing MAT4-His with GST-MAT1, -MAT2, -MAT3, -MAT4, or GST itself (as a negative control) and immunoprecipitated with Glutathione-Sepharose beads. The co-IP proteins were immunoblotted with anti-His and anti-GST antibodies. C, Gel filtration analyses. The 0.5 mg of total proteins extracted from ∼20 g of the 15-d-old seedlings of MAT4-FLAG was applied to an ANTI-FLAG M1 Agarose Affinity Gel. The proteins were eluted using 0.5 µg/µL FLAG Peptide. The elution at the peaks was used for LC-MS analysis. D, LC-MS/MS analyses of the proteins of the three peaks in C. Cov indicates the percentage of sequence coverage (%); Seq (sig) indicates number of significant sequences.
    Figure Legend Snippet: MAT4 interacts with different MATs in plants. A, MAT4 interacted with MAT1, MAT2, MAT3, or MAT4 itself in a protein co-IP assay. Total proteins were extracted from Arabidopsis protoplasts transiently coexpressing the MAT4-FLAG with MAT1-, MAT2-, MAT3-, MAT4-GFP, or GFP (as a negative control) plasmids and immunoprecipitated with anti-GFP beads. The co-IP proteins were immunoblotted with anti-FLAG and anti-GFP antibodies. B, Protein pull-down assay for MAT4 interaction with MAT1, MAT2, MAT3, or MAT4 itself. Total proteins were isolated from E. coli coexpressing MAT4-His with GST-MAT1, -MAT2, -MAT3, -MAT4, or GST itself (as a negative control) and immunoprecipitated with Glutathione-Sepharose beads. The co-IP proteins were immunoblotted with anti-His and anti-GST antibodies. C, Gel filtration analyses. The 0.5 mg of total proteins extracted from ∼20 g of the 15-d-old seedlings of MAT4-FLAG was applied to an ANTI-FLAG M1 Agarose Affinity Gel. The proteins were eluted using 0.5 µg/µL FLAG Peptide. The elution at the peaks was used for LC-MS analysis. D, LC-MS/MS analyses of the proteins of the three peaks in C. Cov indicates the percentage of sequence coverage (%); Seq (sig) indicates number of significant sequences.

    Techniques Used: Co-Immunoprecipitation Assay, Negative Control, Immunoprecipitation, Pull Down Assay, Isolation, Filtration, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Sequencing

    15) Product Images from "Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum"

    Article Title: Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum

    Journal: Microbial Genomics

    doi: 10.1099/mgen.0.000345

    Orthologous proteins analysis of ABC family transporters in C. minitans and related fungal genomes. (a) Analysis of orthologous groups of ABC transporters in C. minitans , Trichoderma spp. and plant pathogenic fungi. (b) Identified DEGs of transporters during the early stages of mycoparasitism. PDR: Pleiotropic drug resistance, EPP: Eye pigment precursor transporter, Gld: Gliding motility ABC transporter, CPR: Cholesterol/phospholipid/retinal flippase, TauT: Taurine Uptake Transporter, U-ABC1: Unknown-ABC1, DrugE1: Drug exporter-1, BIT: Brachyspira Iron Transporter, B12-P: Cobalamine Precursor, PepT: Peptide/Opine/Nickel Uptake Transporter, PAAT: Polar Amino Acid Uptake Transporter, EVE: Ethyl Viologen Exporter, STE: a-Factor sex pheromone exporter, MPE: Mitochondrial peptide exporter, P-FAT: Peroxysomal fatty acyl CoA transporter, HMT: Heavy metal transporter, DCT: Drug conjugate transporter, MDR: Multidrug resistance exporter, DrugRA1: Drug resistance ATPase-1, DrugRA2: Drug resistance ATPase-2. The species-specific proteins encoding genes expression in C. minitans was represented of the black triangle; the blue box represented the gene of ABC transporters of the shared orthologous groups of C. minitans with Trichoderma spp. (c) qRT-PCR valued the DEGs of three ABC transporters encoding genes. 0, 4 h and 12 h p.i. represent different mycoparasitic time points of C. minitans parasitizing on the hyphae of S. sclerotiorum . The black lines represent the RPKM value of the genes in RNA-seq and the bars show the qRT-PCR results of the DEGs. Error bars indicate the standard deviation of three replicates.
    Figure Legend Snippet: Orthologous proteins analysis of ABC family transporters in C. minitans and related fungal genomes. (a) Analysis of orthologous groups of ABC transporters in C. minitans , Trichoderma spp. and plant pathogenic fungi. (b) Identified DEGs of transporters during the early stages of mycoparasitism. PDR: Pleiotropic drug resistance, EPP: Eye pigment precursor transporter, Gld: Gliding motility ABC transporter, CPR: Cholesterol/phospholipid/retinal flippase, TauT: Taurine Uptake Transporter, U-ABC1: Unknown-ABC1, DrugE1: Drug exporter-1, BIT: Brachyspira Iron Transporter, B12-P: Cobalamine Precursor, PepT: Peptide/Opine/Nickel Uptake Transporter, PAAT: Polar Amino Acid Uptake Transporter, EVE: Ethyl Viologen Exporter, STE: a-Factor sex pheromone exporter, MPE: Mitochondrial peptide exporter, P-FAT: Peroxysomal fatty acyl CoA transporter, HMT: Heavy metal transporter, DCT: Drug conjugate transporter, MDR: Multidrug resistance exporter, DrugRA1: Drug resistance ATPase-1, DrugRA2: Drug resistance ATPase-2. The species-specific proteins encoding genes expression in C. minitans was represented of the black triangle; the blue box represented the gene of ABC transporters of the shared orthologous groups of C. minitans with Trichoderma spp. (c) qRT-PCR valued the DEGs of three ABC transporters encoding genes. 0, 4 h and 12 h p.i. represent different mycoparasitic time points of C. minitans parasitizing on the hyphae of S. sclerotiorum . The black lines represent the RPKM value of the genes in RNA-seq and the bars show the qRT-PCR results of the DEGs. Error bars indicate the standard deviation of three replicates.

    Techniques Used: HMT Assay, Expressing, Quantitative RT-PCR, RNA Sequencing Assay, Standard Deviation

    Distribution of the MFS transporters in the C. minitans ZS-1 genome and the DEGs involved in mycoparasitism. (a) Orthologous proteins groups distribution of SP, ACS, DHA1, DHA2, MCT and NAG-T in MFS transporters in three groups of Cm, Tr and Pa. (b) Gene expression of MFS transporters, which detected significantly changed during the mycoparasitism stages of 0, 4 and 12 h, respectively, in C. minitans . SP: Sugar Porter Family, ACS: Anion:Cation Symporter Family, DHA1: Drug:H+Antiporter-1 (12 Spanner) Family, DHA2: Drug:H+Antiporter-2 (14 Spanner) Family, MCT: Monocarboxylate Transporter Family, NAG-T: N-Acetylglucosamine Transporter Family, FHS: Fucose: H+Symporter Family, PHS: Phosphate: H+Symporter Family, OCT, Organic Cation Transporter Family, V-BAAT, Vacuolar Basic Amino Acid Transporter Family, SIT: Siderophore-Iron Transporter Family, LplT: Lysophospholipid Transporter Family, NNP: Nitrate/Nitrite Porter family, UMF1: Unidentified Major Facilitator-1 Family, LAT3: l -Amino Acid Transporter-3 Family, UMF12: Unidentified Major Facilitator-12 Family, UMF23: Unidentified Major Facilitator-23 Family, MHS: Metabolite:H+Symporter Family, SHS: Sialate:H+Symporter Family, FLVCR: Feline Leukemia Virus Subgroup C Receptor/Heme Importer Family, DCP: Major Facilitator Superfamily Domain-containing Protein 5 Family, Pl-Cu-UP: Plant Copper Uptake Porter, UMF30: Unidentified Major Facilitator-30 Family, YnfM: Acriflavin-sensitivity Family, PAT: Peptide/Acetyl-Coenzyme A/Drug Transporter Family, OFA: Oxalate:Formate Antiporter Family, ACDE: Aromatic Compound/Drug Exporter Family, PCFT/HCP: Proton Coupled Folate Transporter/Heme Carrier Protein Family, Pht: Proteobacterial Intraphagosomal Amino Acid Transporter Family. Sclsc2, S. sclerotiorum strain 1980; Sclbo1, S. borealis ; BcDW1, B. cinerea strain DW1; B05.10, B. cinerea strain B05.10; BcT4, B. cinerea strain T4; Parno2, P. nodorum strain SN15; Pyrtr1, P. tritici-repentis strain Pt-1C-BFP; Triat2, T. atroviride ; Triha1, T. harzianum ; Trivi2, T. virens ; CMZSB, C. minitans strain ZS-1 (this research); Parsp1, P. sporulosa . Cm, orthologous groups of MFS transporters in C. minitans ; Tr, orthologous groups of MFS transporters in Trichoderma spp.; and Pa, orthologous groups of MFS transporters in plant pathogenic fungi.
    Figure Legend Snippet: Distribution of the MFS transporters in the C. minitans ZS-1 genome and the DEGs involved in mycoparasitism. (a) Orthologous proteins groups distribution of SP, ACS, DHA1, DHA2, MCT and NAG-T in MFS transporters in three groups of Cm, Tr and Pa. (b) Gene expression of MFS transporters, which detected significantly changed during the mycoparasitism stages of 0, 4 and 12 h, respectively, in C. minitans . SP: Sugar Porter Family, ACS: Anion:Cation Symporter Family, DHA1: Drug:H+Antiporter-1 (12 Spanner) Family, DHA2: Drug:H+Antiporter-2 (14 Spanner) Family, MCT: Monocarboxylate Transporter Family, NAG-T: N-Acetylglucosamine Transporter Family, FHS: Fucose: H+Symporter Family, PHS: Phosphate: H+Symporter Family, OCT, Organic Cation Transporter Family, V-BAAT, Vacuolar Basic Amino Acid Transporter Family, SIT: Siderophore-Iron Transporter Family, LplT: Lysophospholipid Transporter Family, NNP: Nitrate/Nitrite Porter family, UMF1: Unidentified Major Facilitator-1 Family, LAT3: l -Amino Acid Transporter-3 Family, UMF12: Unidentified Major Facilitator-12 Family, UMF23: Unidentified Major Facilitator-23 Family, MHS: Metabolite:H+Symporter Family, SHS: Sialate:H+Symporter Family, FLVCR: Feline Leukemia Virus Subgroup C Receptor/Heme Importer Family, DCP: Major Facilitator Superfamily Domain-containing Protein 5 Family, Pl-Cu-UP: Plant Copper Uptake Porter, UMF30: Unidentified Major Facilitator-30 Family, YnfM: Acriflavin-sensitivity Family, PAT: Peptide/Acetyl-Coenzyme A/Drug Transporter Family, OFA: Oxalate:Formate Antiporter Family, ACDE: Aromatic Compound/Drug Exporter Family, PCFT/HCP: Proton Coupled Folate Transporter/Heme Carrier Protein Family, Pht: Proteobacterial Intraphagosomal Amino Acid Transporter Family. Sclsc2, S. sclerotiorum strain 1980; Sclbo1, S. borealis ; BcDW1, B. cinerea strain DW1; B05.10, B. cinerea strain B05.10; BcT4, B. cinerea strain T4; Parno2, P. nodorum strain SN15; Pyrtr1, P. tritici-repentis strain Pt-1C-BFP; Triat2, T. atroviride ; Triha1, T. harzianum ; Trivi2, T. virens ; CMZSB, C. minitans strain ZS-1 (this research); Parsp1, P. sporulosa . Cm, orthologous groups of MFS transporters in C. minitans ; Tr, orthologous groups of MFS transporters in Trichoderma spp.; and Pa, orthologous groups of MFS transporters in plant pathogenic fungi.

    Techniques Used: Expressing

    Statistical analysis of DEGs in C. minitans induced by hyphae of S. sclerotiorum and confirmation of the gene-expression pattern of the DEGs using qRT-PCR. (a) Based on the RPKM value, the heatmap of all the DEGs detected of C. minitans at the early stages with 0, 4 and 12 h induced by S. sclerotiorum . The detailed DEG list is presented in Table S3. (b) The statistical number of the up-regulated and down-regulated DEGs in the comparison pairwise of 4 h p.i. (CmSs0-4) and 12 h p.i. (CmSs0-12) to the control set of 0 h p.i. and 12 h p.i. to 4 h p.i. (CmSs4-12). (c) The common and particular DEGs in comparison groups of CmSs0-4, CmSs0-12 and CmSs4-12. (d) Confirmation of gene-expression pattern in C. minitans . Mycelial RNA of C. minitans parasitizing on S. sclerotiorum at 0, 4 or 12 h p.i. was used. The black bars represent the RPKM value of the genes in RNA-seq and the bars in grey shades show the qRT-PCR results of the DEGs. Error bars indicate the standard deviation of three replicates.
    Figure Legend Snippet: Statistical analysis of DEGs in C. minitans induced by hyphae of S. sclerotiorum and confirmation of the gene-expression pattern of the DEGs using qRT-PCR. (a) Based on the RPKM value, the heatmap of all the DEGs detected of C. minitans at the early stages with 0, 4 and 12 h induced by S. sclerotiorum . The detailed DEG list is presented in Table S3. (b) The statistical number of the up-regulated and down-regulated DEGs in the comparison pairwise of 4 h p.i. (CmSs0-4) and 12 h p.i. (CmSs0-12) to the control set of 0 h p.i. and 12 h p.i. to 4 h p.i. (CmSs4-12). (c) The common and particular DEGs in comparison groups of CmSs0-4, CmSs0-12 and CmSs4-12. (d) Confirmation of gene-expression pattern in C. minitans . Mycelial RNA of C. minitans parasitizing on S. sclerotiorum at 0, 4 or 12 h p.i. was used. The black bars represent the RPKM value of the genes in RNA-seq and the bars in grey shades show the qRT-PCR results of the DEGs. Error bars indicate the standard deviation of three replicates.

    Techniques Used: Expressing, Quantitative RT-PCR, RNA Sequencing Assay, Standard Deviation

    Gene expression and core biosynthetic genes related to secondary metabolism in C. minitans during the early stages of mycoparasitism. (a) Structures of core NRPS biosynthetic proteins predicted to be involved in mycoparasitism in C. minitans strain ZS-1. A: adenylation (AMP) domain; C: condensation domain; PCP: peptidyl-carrier protein domain; cMT: cycle methyltransferase; NAD: nicotinamide adenine dinucleotide; E: epimerization domain. (b) Structures of core PKS or hybrid PKS-NRPS biosynthetic proteins predicted to be involved in mycoparasitism in C. minitans strain ZS-1. KS: beta-ketoacyl-synthase domain; AT: acyl transferase domain; DH: polyketide synthase dehydrogenase; ER: enoyl reductase domain; KR: ketoreductase domain; TE: thioesterase; ACP: acyl carrier protein; TD: thioesterase domain. (c) Heatmap created with MeV (version 4.9.0) based on the RPKM values of the detected genes in C. minitans strain ZS-1; the RPKM values were normalized within the row for each gene.
    Figure Legend Snippet: Gene expression and core biosynthetic genes related to secondary metabolism in C. minitans during the early stages of mycoparasitism. (a) Structures of core NRPS biosynthetic proteins predicted to be involved in mycoparasitism in C. minitans strain ZS-1. A: adenylation (AMP) domain; C: condensation domain; PCP: peptidyl-carrier protein domain; cMT: cycle methyltransferase; NAD: nicotinamide adenine dinucleotide; E: epimerization domain. (b) Structures of core PKS or hybrid PKS-NRPS biosynthetic proteins predicted to be involved in mycoparasitism in C. minitans strain ZS-1. KS: beta-ketoacyl-synthase domain; AT: acyl transferase domain; DH: polyketide synthase dehydrogenase; ER: enoyl reductase domain; KR: ketoreductase domain; TE: thioesterase; ACP: acyl carrier protein; TD: thioesterase domain. (c) Heatmap created with MeV (version 4.9.0) based on the RPKM values of the detected genes in C. minitans strain ZS-1; the RPKM values were normalized within the row for each gene.

    Techniques Used: Expressing

    Non-redundant (Nr) classification analysis of the encoded proteins in the genome of C. minitans ZS-1. (a) and (b) represent the similarity distribution and species distribution of the Nr annotation based on the blast hit number, respectively. Parsp1, P. sporulosa ; Perma1, P. macrospinosa ; Corca1, C. cassiicola Philippines; Cloaq1, C. aquaticus ; PyrDS1, Pyrenochaeta sp. DS3sAY3a; Altal1, Alternaria alternate ; StaSR1, S tagonospora sp. SRC1lsM3a; Ascra1, Ascochyta rabiei ; Epini1, Epicoccum nigrum ; Parno2, Parastagonospora nodorum ; Stely1, Stemphylium lycopersici , Pyrtr1, Pyrenophora tritici-repentis ; other, the rest of the 185 species matched five or more blast hits (Table S8).
    Figure Legend Snippet: Non-redundant (Nr) classification analysis of the encoded proteins in the genome of C. minitans ZS-1. (a) and (b) represent the similarity distribution and species distribution of the Nr annotation based on the blast hit number, respectively. Parsp1, P. sporulosa ; Perma1, P. macrospinosa ; Corca1, C. cassiicola Philippines; Cloaq1, C. aquaticus ; PyrDS1, Pyrenochaeta sp. DS3sAY3a; Altal1, Alternaria alternate ; StaSR1, S tagonospora sp. SRC1lsM3a; Ascra1, Ascochyta rabiei ; Epini1, Epicoccum nigrum ; Parno2, Parastagonospora nodorum ; Stely1, Stemphylium lycopersici , Pyrtr1, Pyrenophora tritici-repentis ; other, the rest of the 185 species matched five or more blast hits (Table S8).

    Techniques Used:

    Comparison of CAZymes encoded in C. minitans ZS-1 and other 38 ascomycetes. (a) Multivariate grouping of ascomycete fungal genomes based on the protein number profiles of predicted CAZyme families using PCA. The CAZyme proteins from the fungal genomes were identified against the CAZy database. A number list of all CAZyme proteins in each genome is shown in Table S10. (b) Orthologous analysis of PCWDE-related protein comparison of C. minitans (Cm) with Trichoderma spp. (Tr) and seven plant pathogenic fungi (Pa); (c) PCWDE-related protein comparison of Cm with Tr and Pa. Orthologous groups were determined among the CAZymes encoded in the genomes of C. minitans , three Trichoderma spp. ( T. atroviride , T. harzianum and T. virens ) and seven plant pathogenic fungi ( S. sclerotiorum strain 1980, S. borealis , B. cinerea strain DW1, B. cinerea strain B05.10, B. cinerea strain BcT4, P. nodorum strain SN15, and P. tritici-repentis strain Pt-1C-BFP) (details in Table S6). P(F)CWDEs, plant (fungus) cell-wall-degrading enzymes. Cm, CAZyme orthologous groups related to the cell wall in C. minitans ; Tr, CAZyme groups related to cell wall encoded in Trichoderma spp.; Pa, CAZyme orthologous groups encoded by the seven plant pathogenic fungi genomes.
    Figure Legend Snippet: Comparison of CAZymes encoded in C. minitans ZS-1 and other 38 ascomycetes. (a) Multivariate grouping of ascomycete fungal genomes based on the protein number profiles of predicted CAZyme families using PCA. The CAZyme proteins from the fungal genomes were identified against the CAZy database. A number list of all CAZyme proteins in each genome is shown in Table S10. (b) Orthologous analysis of PCWDE-related protein comparison of C. minitans (Cm) with Trichoderma spp. (Tr) and seven plant pathogenic fungi (Pa); (c) PCWDE-related protein comparison of Cm with Tr and Pa. Orthologous groups were determined among the CAZymes encoded in the genomes of C. minitans , three Trichoderma spp. ( T. atroviride , T. harzianum and T. virens ) and seven plant pathogenic fungi ( S. sclerotiorum strain 1980, S. borealis , B. cinerea strain DW1, B. cinerea strain B05.10, B. cinerea strain BcT4, P. nodorum strain SN15, and P. tritici-repentis strain Pt-1C-BFP) (details in Table S6). P(F)CWDEs, plant (fungus) cell-wall-degrading enzymes. Cm, CAZyme orthologous groups related to the cell wall in C. minitans ; Tr, CAZyme groups related to cell wall encoded in Trichoderma spp.; Pa, CAZyme orthologous groups encoded by the seven plant pathogenic fungi genomes.

    Techniques Used:

    Expression of FCWDEs in the CAZymes detected during mycoparasitism. (a) The FCWDE-encoding genes among the DEGs of C. minitans induced by the hyphae of S. sclerotiorum at the early mycoparasitism time points of 0, 4 and 12 h. (b) Quantitative RT-PCR amplification of FCWDE-encoding DEGs of C. minitans . The black lines represent the RPKM value of the genes in RNA-seq and the bars show the qRT-PCR results of the DEGs. Error bars indicate the standard deviation of three replicates.
    Figure Legend Snippet: Expression of FCWDEs in the CAZymes detected during mycoparasitism. (a) The FCWDE-encoding genes among the DEGs of C. minitans induced by the hyphae of S. sclerotiorum at the early mycoparasitism time points of 0, 4 and 12 h. (b) Quantitative RT-PCR amplification of FCWDE-encoding DEGs of C. minitans . The black lines represent the RPKM value of the genes in RNA-seq and the bars show the qRT-PCR results of the DEGs. Error bars indicate the standard deviation of three replicates.

    Techniques Used: Expressing, Quantitative RT-PCR, Amplification, RNA Sequencing Assay, Standard Deviation

    Serine peptidase secreted proteins in the mycoparasitism process in C. minitans . (a) Enriched GO terms' graph of serine peptidase of the DEG-encoding secreted proteins. (b) Expression of the unique DEGs involved in GO: 0003824. (c) Expression of the unique DEGs involved in hydrolase activity in GO molecular function. (d) Expression of the unique DEGs related to GO: 0140096 and GO: 0008233, with CMZSB_08830 in GO: 0140096. (e) Expression of the five DEGs related to each of GO: 0017171, GO: 0070011 and GO: 0008236. The graph of GO terms was downloaded and modified from https://www.ebi.ac.uk/QuickGO.
    Figure Legend Snippet: Serine peptidase secreted proteins in the mycoparasitism process in C. minitans . (a) Enriched GO terms' graph of serine peptidase of the DEG-encoding secreted proteins. (b) Expression of the unique DEGs involved in GO: 0003824. (c) Expression of the unique DEGs involved in hydrolase activity in GO molecular function. (d) Expression of the unique DEGs related to GO: 0140096 and GO: 0008233, with CMZSB_08830 in GO: 0140096. (e) Expression of the five DEGs related to each of GO: 0017171, GO: 0070011 and GO: 0008236. The graph of GO terms was downloaded and modified from https://www.ebi.ac.uk/QuickGO.

    Techniques Used: Expressing, Activity Assay, Modification

    16) Product Images from "Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress"

    Article Title: Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress

    Journal: bioRxiv

    doi: 10.1101/2020.08.07.242172

    F L OE1 and FLOE1 expression in Arabidopsis . (A) Tissue-specific expression of FLOE1 derived from ePlant ( 37 ). (B) RT-qPCR analysis of different developmental stages shows peak expression in mature dry seeds, and a decrease in expression upon imbibition. “Dark”, “green” and “yellow” refer to the maturation stages of the siliques (from younger to older), which roughly correspond to 4-7, 8-10 and 11-13 days post-anthesis ( 22 ), and “imbibed” corresponds to seeds that were imbibed in sterile double-distilled water for 24 h. Col-0 (WT) plants were used. One-way ANOVA. **** p-value
    Figure Legend Snippet: F L OE1 and FLOE1 expression in Arabidopsis . (A) Tissue-specific expression of FLOE1 derived from ePlant ( 37 ). (B) RT-qPCR analysis of different developmental stages shows peak expression in mature dry seeds, and a decrease in expression upon imbibition. “Dark”, “green” and “yellow” refer to the maturation stages of the siliques (from younger to older), which roughly correspond to 4-7, 8-10 and 11-13 days post-anthesis ( 22 ), and “imbibed” corresponds to seeds that were imbibed in sterile double-distilled water for 24 h. Col-0 (WT) plants were used. One-way ANOVA. **** p-value

    Techniques Used: Expressing, Derivative Assay, Quantitative RT-PCR

    17) Product Images from "In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes"

    Article Title: In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes

    Journal: Plants

    doi: 10.3390/plants6040052

    Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.
    Figure Legend Snippet: Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.

    Techniques Used: DNA Extraction, Modification

    Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.
    Figure Legend Snippet: Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.

    Techniques Used: DNA Extraction, Modification

    18) Product Images from "Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species"

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species

    Journal:

    doi:

    Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;
    Figure Legend Snippet: Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;

    Techniques Used: DNA Extraction, Infection, Polymerase Chain Reaction

    19) Product Images from "Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species"

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species

    Journal:

    doi:

    Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;
    Figure Legend Snippet: Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;

    Techniques Used: DNA Extraction, Infection, Polymerase Chain Reaction

    20) Product Images from "In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes"

    Article Title: In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes

    Journal: Plants

    doi: 10.3390/plants6040052

    Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.
    Figure Legend Snippet: Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.

    Techniques Used: DNA Extraction, Modification

    21) Product Images from "Filter paper-based spin column method for cost-efficient DNA or RNA purification"

    Article Title: Filter paper-based spin column method for cost-efficient DNA or RNA purification

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0203011

    The efficiency of filter paper for purification of nucleic acids from various sources using respective Qiagen kits. (A) Tomato genomic DNAs purified using Qiagen DNeasy plant mini kit. (B) Tomato total RNAs purified using Qiagen RNeasy plant mini kit. (C) PCR products of a GUS fragment purified using Qiagen QIAquick PCR purification kit. (D) PCR products of GUS fragment recovered from an agarose gel using a Qiagen QIAquick gel extraction kit. (E) pUC -19 plasmid DNAs purified using a Qiagen QIAprep spin miniprep kit. For each panel, from left to right are (Q) nucleic acid purified in experiments using original Qiagen spin column, (G) reassembled spin column using two layers of Whatman glass microfiber filters (Grade GF/F), and (P) reassembled spin column using two layers of Whatman qualitative filter paper, (Grade 3) respectively. Upper panel is quantification data based on three experimental replicates normalized according to performance of the Qiagen kit; lower panel is an image of agarose gel electrophoresis for the same volume of purified nucleic acids.
    Figure Legend Snippet: The efficiency of filter paper for purification of nucleic acids from various sources using respective Qiagen kits. (A) Tomato genomic DNAs purified using Qiagen DNeasy plant mini kit. (B) Tomato total RNAs purified using Qiagen RNeasy plant mini kit. (C) PCR products of a GUS fragment purified using Qiagen QIAquick PCR purification kit. (D) PCR products of GUS fragment recovered from an agarose gel using a Qiagen QIAquick gel extraction kit. (E) pUC -19 plasmid DNAs purified using a Qiagen QIAprep spin miniprep kit. For each panel, from left to right are (Q) nucleic acid purified in experiments using original Qiagen spin column, (G) reassembled spin column using two layers of Whatman glass microfiber filters (Grade GF/F), and (P) reassembled spin column using two layers of Whatman qualitative filter paper, (Grade 3) respectively. Upper panel is quantification data based on three experimental replicates normalized according to performance of the Qiagen kit; lower panel is an image of agarose gel electrophoresis for the same volume of purified nucleic acids.

    Techniques Used: Purification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Gel Extraction, Plasmid Preparation

    22) Product Images from "A Transcript Profiling Approach Reveals an Abscisic Acid-Specific Glycosyltransferase (UGT73C14) Induced in Developing Fiber of Ligon lintless-2 Mutant of Cotton (Gossypium hirsutum L.)"

    Article Title: A Transcript Profiling Approach Reveals an Abscisic Acid-Specific Glycosyltransferase (UGT73C14) Induced in Developing Fiber of Ligon lintless-2 Mutant of Cotton (Gossypium hirsutum L.)

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0075268

    Copy Number Variation Assay of UGT73C14 using the single copy GhMYB25 as a reference gene. Genomic DNA was isolated from frozen leaf tissues using Qiagen DNeasy DNA extraction kit, and subjected to a 5 cycle Specific Template Amplification (STA) reaction. The STA reaction product was then subject to Taqman digital PCR following the manufacturer’s recommendations and microfluidic chips provided by Fluidigm. A ratio of UGT73C14 positive wells to GhMYB25 positive wells determined the relative copy number. To determine the copy number (y-axis values), for tetraploid lines (G. hirsutum ), the UGT73C14/GhMYB25 ratio was multiplied by four, and for diploid lines (G. raimondii, G . herbaceum and G . arboreum ), the UGT73C14/GhMYB25 ratio was muliplied by two. Error Bars represents the 95% Confidence Interval.
    Figure Legend Snippet: Copy Number Variation Assay of UGT73C14 using the single copy GhMYB25 as a reference gene. Genomic DNA was isolated from frozen leaf tissues using Qiagen DNeasy DNA extraction kit, and subjected to a 5 cycle Specific Template Amplification (STA) reaction. The STA reaction product was then subject to Taqman digital PCR following the manufacturer’s recommendations and microfluidic chips provided by Fluidigm. A ratio of UGT73C14 positive wells to GhMYB25 positive wells determined the relative copy number. To determine the copy number (y-axis values), for tetraploid lines (G. hirsutum ), the UGT73C14/GhMYB25 ratio was multiplied by four, and for diploid lines (G. raimondii, G . herbaceum and G . arboreum ), the UGT73C14/GhMYB25 ratio was muliplied by two. Error Bars represents the 95% Confidence Interval.

    Techniques Used: Isolation, DNA Extraction, Amplification, Digital PCR

    23) Product Images from "Cloning of a functional mannose-6-phosphate reductase (M6PR) gene homolog from Egyptian celery plants (Apium graveolens): overexpression in non-mannitol producing plants resulted in mannitol accumulation in transgenic individuals"

    Article Title: Cloning of a functional mannose-6-phosphate reductase (M6PR) gene homolog from Egyptian celery plants (Apium graveolens): overexpression in non-mannitol producing plants resulted in mannitol accumulation in transgenic individuals

    Journal: 3 Biotech

    doi: 10.1007/s13205-017-0975-3

    a Chromatogram for the soluble sugars in the negative control sample. b Chromatogram of mannitol in the transgenic tobacco sample. In b the mannitol peak is indicated with a red circle
    Figure Legend Snippet: a Chromatogram for the soluble sugars in the negative control sample. b Chromatogram of mannitol in the transgenic tobacco sample. In b the mannitol peak is indicated with a red circle

    Techniques Used: Negative Control, Transgenic Assay

    a PCR screening of putative transgenic tobacco shoots, white arrows indicating positive samples. b RT-PCR of the positive tobacco plants indicating the presence of M6PR transcripts in 9 out of the 10 plants tested
    Figure Legend Snippet: a PCR screening of putative transgenic tobacco shoots, white arrows indicating positive samples. b RT-PCR of the positive tobacco plants indicating the presence of M6PR transcripts in 9 out of the 10 plants tested

    Techniques Used: Polymerase Chain Reaction, Transgenic Assay, Reverse Transcription Polymerase Chain Reaction

    Different stages of transgenic tobacco shoots development. a Regeneration of tobacco shoots on regeneration medium. b Well-developed shoots on rooting medium. c Transformed shoots acclimatized in small pots in growth chamber. d Fully developed tobacco plants with flowers
    Figure Legend Snippet: Different stages of transgenic tobacco shoots development. a Regeneration of tobacco shoots on regeneration medium. b Well-developed shoots on rooting medium. c Transformed shoots acclimatized in small pots in growth chamber. d Fully developed tobacco plants with flowers

    Techniques Used: Transgenic Assay, Transformation Assay

    24) Product Images from "The Arabidopsis acetylated histone-binding protein BRAT1 forms a complex with BRP1 and prevents transcriptional silencing"

    Article Title: The Arabidopsis acetylated histone-binding protein BRAT1 forms a complex with BRP1 and prevents transcriptional silencing

    Journal: Nature Communications

    doi: 10.1038/ncomms11715

    DNA demethylation loci targeted by BRAT1 and BRP1. ( a ) Numbers of overlapping hyper-DMRs among brat1-1 , brp1-1 and ros1-4 mutants. ( b ) Heat maps of DNA methylation levels within brat1-1 hyper-DMRs. The columns represent the indicated genotypes, and the rows represent the differentially methylated loci. Light yellow indicates low methylation, and black indicates high methylation. ( c ) Composition of the genomic location of the hyper-DMRs in the brat1-1 , brp1-1 and ros1-4 mutants. TE, transposable element. ( d ) Plots indicate CG, CHG and CHH methylation at genes and their 1-kb upstream and downstream regions in the wild type (WT). Red lines indicate DNA methylation of all genes in Arabidopsis , and blue, green and brown lines indicate DNA methylation of genes with hyper-DMRs in brat1 , brp1 and ros1 , respectively. TSS, transcription start site; TTS, transcription termination site. ( e ) The DNA methylation level of the ROS1 promoter region was calculated based on the whole-genome bisulfite sequencing data. The methylation levels of the boxed region are shown by the histograms for WT, brat1-1 , brp1-1 and ros1-4 . The yellow box indicates the TE region in the ROS1 promoter. ( f ) The DNA methylation levels of DT414 , DT231 , DT539 and AT3TE92795 as determined by locus-specific bisulfite sequencing analyses.
    Figure Legend Snippet: DNA demethylation loci targeted by BRAT1 and BRP1. ( a ) Numbers of overlapping hyper-DMRs among brat1-1 , brp1-1 and ros1-4 mutants. ( b ) Heat maps of DNA methylation levels within brat1-1 hyper-DMRs. The columns represent the indicated genotypes, and the rows represent the differentially methylated loci. Light yellow indicates low methylation, and black indicates high methylation. ( c ) Composition of the genomic location of the hyper-DMRs in the brat1-1 , brp1-1 and ros1-4 mutants. TE, transposable element. ( d ) Plots indicate CG, CHG and CHH methylation at genes and their 1-kb upstream and downstream regions in the wild type (WT). Red lines indicate DNA methylation of all genes in Arabidopsis , and blue, green and brown lines indicate DNA methylation of genes with hyper-DMRs in brat1 , brp1 and ros1 , respectively. TSS, transcription start site; TTS, transcription termination site. ( e ) The DNA methylation level of the ROS1 promoter region was calculated based on the whole-genome bisulfite sequencing data. The methylation levels of the boxed region are shown by the histograms for WT, brat1-1 , brp1-1 and ros1-4 . The yellow box indicates the TE region in the ROS1 promoter. ( f ) The DNA methylation levels of DT414 , DT231 , DT539 and AT3TE92795 as determined by locus-specific bisulfite sequencing analyses.

    Techniques Used: DNA Methylation Assay, Methylation, Methylation Sequencing

    25) Product Images from "GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing"

    Article Title: GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2016.01350

    Agarose gel image showing the PCR products amplified from markers designed by GMATA . Lanes 1–10 represent the PCR amplicons from the DNA of tobacco species or varieties N. sylvestris, N. tomentosiformis, N. tabacum HD, N. tabacum K326, and N. benthamiana and N. tabacum varieties Yunyan-85, Yunyan-97, Zhongyan-100, KRK26 and CB-1.
    Figure Legend Snippet: Agarose gel image showing the PCR products amplified from markers designed by GMATA . Lanes 1–10 represent the PCR amplicons from the DNA of tobacco species or varieties N. sylvestris, N. tomentosiformis, N. tabacum HD, N. tabacum K326, and N. benthamiana and N. tabacum varieties Yunyan-85, Yunyan-97, Zhongyan-100, KRK26 and CB-1.

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification

    26) Product Images from "Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W]Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W] [OA]"

    Article Title: Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W]Target of Rapamycin Regulates Development and Ribosomal RNA Expression through Kinase Domain in Arabidopsis 1 [W] [OA]

    Journal: Plant Physiology

    doi: 10.1104/pp.110.169045

    TOR interacts with the promoter and 5′-ETS of the ribosome RNA gene and regulates ribosome rRNA expression in Arabidopsis. A, The organization of the 45S rRNA gene in Arabidopsis and the location of 18 overlapping PCR fragments spanning 45S rRNA
    Figure Legend Snippet: TOR interacts with the promoter and 5′-ETS of the ribosome RNA gene and regulates ribosome rRNA expression in Arabidopsis. A, The organization of the 45S rRNA gene in Arabidopsis and the location of 18 overlapping PCR fragments spanning 45S rRNA

    Techniques Used: Expressing, Polymerase Chain Reaction

    27) Product Images from "Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia 1 1 [W] 1 [W] [OPEN]"

    Article Title: Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia 1 1 [W] 1 [W] [OPEN]

    Journal: Plant Physiology

    doi: 10.1104/pp.114.242826

    Illustration of a model suggesting EPSPS amplifications via unequal crossover in response to glyphosate selection and evolution of glyphosate resistance in K. scoparia .
    Figure Legend Snippet: Illustration of a model suggesting EPSPS amplifications via unequal crossover in response to glyphosate selection and evolution of glyphosate resistance in K. scoparia .

    Techniques Used: Selection

    EPSPS genomic copies and level of glyphosate resistance in K. scoparia plants collected in 2007, 2010, and 2012.
    Figure Legend Snippet: EPSPS genomic copies and level of glyphosate resistance in K. scoparia plants collected in 2007, 2010, and 2012.

    Techniques Used:

    plants to a glyphosate rate of 868 g ae ha –1 . B, Relationship between EPSPS (squares), and six F1 plants (diamonds) of K. scoparia . EPSPS
    Figure Legend Snippet: plants to a glyphosate rate of 868 g ae ha –1 . B, Relationship between EPSPS (squares), and six F1 plants (diamonds) of K. scoparia . EPSPS

    Techniques Used:

    mapping of EPSPS (B and D) K. scoparia signal showing faint EPSPS signal on the distal end. B, Somatic metaphase spreads
    Figure Legend Snippet: mapping of EPSPS (B and D) K. scoparia signal showing faint EPSPS signal on the distal end. B, Somatic metaphase spreads

    Techniques Used:

    mapping of EPSPS (GR2) K. scoparia showing EPSPS copies clustered at the distal end of homologous chromosomes. D and E, Hybridization of two colored (red and green)
    Figure Legend Snippet: mapping of EPSPS (GR2) K. scoparia showing EPSPS copies clustered at the distal end of homologous chromosomes. D and E, Hybridization of two colored (red and green)

    Techniques Used: Hybridization

    28) Product Images from "An Easy, Rapid, and Cost-Effective Method for DNA Extraction from Various Lichen Taxa and Specimens Suitable for Analysis of Fungal and Algal Strains"

    Article Title: An Easy, Rapid, and Cost-Effective Method for DNA Extraction from Various Lichen Taxa and Specimens Suitable for Analysis of Fungal and Algal Strains

    Journal: Mycobiology

    doi: 10.5941/MYCO.2014.42.4.311

    Electropherograms of PCR products amplified using 12 representative DNA samples species extracted using our KCl method, and the commercial kit. Comparison of DNA samples extracted with our KCl method (on left) and commercial kit (on right). PCR amplifications were as follows: A, large subunit RNA (LSU) region; B, small subunit RNA (SSU) region; and C, internal transcribed spacer (ITS) specific fungal and algal primer region; upper and lower gel sections show fungi and algae, respectively. Asterisks: Five amplified PCR products generated by our KCl method were selected for sequencing fungal and algal ITS regions. These sequences were registered in GenBank. Representative lichen species: 007293, Flavoparmelia carperata ; 007742, Heterodermia diadermata ; 000978, Heterodermia hypoleuca ; 009659, Lobaria discolor ; 008278, Lobaria retigera ; 001899, Peltigera praetextata ; 011648, Myelochroa entotheiochroa ; 011592, Myelochroa irrugans ; 016180, Parmotrema tinctorum ; 010394, Peltigera polydactylon ; 007637, Punctelia subflava ; 007349, Umbilicaria esculenta .
    Figure Legend Snippet: Electropherograms of PCR products amplified using 12 representative DNA samples species extracted using our KCl method, and the commercial kit. Comparison of DNA samples extracted with our KCl method (on left) and commercial kit (on right). PCR amplifications were as follows: A, large subunit RNA (LSU) region; B, small subunit RNA (SSU) region; and C, internal transcribed spacer (ITS) specific fungal and algal primer region; upper and lower gel sections show fungi and algae, respectively. Asterisks: Five amplified PCR products generated by our KCl method were selected for sequencing fungal and algal ITS regions. These sequences were registered in GenBank. Representative lichen species: 007293, Flavoparmelia carperata ; 007742, Heterodermia diadermata ; 000978, Heterodermia hypoleuca ; 009659, Lobaria discolor ; 008278, Lobaria retigera ; 001899, Peltigera praetextata ; 011648, Myelochroa entotheiochroa ; 011592, Myelochroa irrugans ; 016180, Parmotrema tinctorum ; 010394, Peltigera polydactylon ; 007637, Punctelia subflava ; 007349, Umbilicaria esculenta .

    Techniques Used: Polymerase Chain Reaction, Amplification, Generated, Sequencing

    PCR product electropherograms of the full-length internal transcribed spacer regions and 26S rRNA ( > 1.0 kb) amplified from representative 26 DNA samples derived from taxa at different taxonomic levels (i.e., genus to subspecies) extracted with our KCl method.
    Figure Legend Snippet: PCR product electropherograms of the full-length internal transcribed spacer regions and 26S rRNA ( > 1.0 kb) amplified from representative 26 DNA samples derived from taxa at different taxonomic levels (i.e., genus to subspecies) extracted with our KCl method.

    Techniques Used: Polymerase Chain Reaction, Amplification, Derivative Assay

    29) Product Images from "A modified SDS-based DNA extraction method from raw soybean"

    Article Title: A modified SDS-based DNA extraction method from raw soybean

    Journal: Bioscience Reports

    doi: 10.1042/BSR20182271

    Comparison of four different DNA extraction methods A 260/280 ratios of DNA extracted with different methods; different lowercase letters indicate significant differences amongst DNA yields in ( A ); M, 1, 2, 3, 4, and B correspond to λ DNA HindIII Marker (TIANGEN, Beijing, China), SDS-based method, CTAB method, DP305 method, DNeasy Plant Mini Kit, and negative control PCR in ( B ).
    Figure Legend Snippet: Comparison of four different DNA extraction methods A 260/280 ratios of DNA extracted with different methods; different lowercase letters indicate significant differences amongst DNA yields in ( A ); M, 1, 2, 3, 4, and B correspond to λ DNA HindIII Marker (TIANGEN, Beijing, China), SDS-based method, CTAB method, DP305 method, DNeasy Plant Mini Kit, and negative control PCR in ( B ).

    Techniques Used: DNA Extraction, Marker, Negative Control, Polymerase Chain Reaction

    30) Product Images from "An Effector from the Cyst Nematode Heterodera schachtii Derepresses Host rRNA Genes by Altering Histone Acetylation [OPEN]"

    Article Title: An Effector from the Cyst Nematode Heterodera schachtii Derepresses Host rRNA Genes by Altering Histone Acetylation [OPEN]

    Journal: The Plant Cell

    doi: 10.1105/tpc.18.00570

    A Subset of VAR1 rRNA Variant Is Derepressed and VAR1:45S pre-rRNA Ratio Is Altered in the Arabidopsis 32E03-L Line. (A) Expression of subtypes of rRNA variants in roots of Arabidopsis 32E03-L line analyzed by SNP analysis. Wild-type roots were used as control. (B) Expression of subtypes of rRNA variants in Arabidopsis wild-type root segments enriched in H. schachtii -induced syncytia analyzed by SNP analysis. Wild-type plants were inoculated with H. schachtii J2s and root segments enriched in H. schachtii -induced syncytia (root+syncytium) and adjacent root segments without syncytia (root-syncytium; control) were dissected at 10 d postinoculation. In (A) and (B) , whole root or root segment cDNA was synthesized, subtypes of rRNA variants were amplified by PCR, gel-eluted, digested with Sph I, Alu I, or Msp I to detect VAR1-6645, VAR2-4302, or VAR3-7122 subtype, respectively. DNA fragments were visualized by 2.5% agarose gel electrophoresis. The experiment comprised at least two biological replicates. Similar results were obtained in the two independent experiments. Data of one representative experiment are shown. (C) Quantification of VAR1 rRNA and 45S pre-rRNA in Arabidopsis 32E03-L line (14 and 18 d old) by qPCR. Wild-type plants were used as control. (D) Quantification of rRNA VAR1 and 45S pre-rRNA in wild-type Arabidopsis root segments enriched in H. schachtii -induced syncytia by qPCR. Wild-type plants were inoculated with H. schachtii J2s and root segments enriched in H. schachtii -induced syncytia (root+syncytium) and adjacent root segments without syncytia (root-syncytium; control) were dissected at 10 d postinoculation. In (C) and (D) , whole roots or root segments cDNA was synthesized, and VAR1 and 45S pre-RNA were quantified by qPCR. ACTIN8 was amplified as reference. The experiments comprised three biological replicates, each consisting of three technical replicates. Similar results were obtained in the three independent experiments. Data of one representative experiment are shown. For (A) to (D) , plants of the tested genotypes/treatments were grown in randomized block designs. For each biological replicate, plants were sampled randomly to prepare pools for each genotype/treatment.
    Figure Legend Snippet: A Subset of VAR1 rRNA Variant Is Derepressed and VAR1:45S pre-rRNA Ratio Is Altered in the Arabidopsis 32E03-L Line. (A) Expression of subtypes of rRNA variants in roots of Arabidopsis 32E03-L line analyzed by SNP analysis. Wild-type roots were used as control. (B) Expression of subtypes of rRNA variants in Arabidopsis wild-type root segments enriched in H. schachtii -induced syncytia analyzed by SNP analysis. Wild-type plants were inoculated with H. schachtii J2s and root segments enriched in H. schachtii -induced syncytia (root+syncytium) and adjacent root segments without syncytia (root-syncytium; control) were dissected at 10 d postinoculation. In (A) and (B) , whole root or root segment cDNA was synthesized, subtypes of rRNA variants were amplified by PCR, gel-eluted, digested with Sph I, Alu I, or Msp I to detect VAR1-6645, VAR2-4302, or VAR3-7122 subtype, respectively. DNA fragments were visualized by 2.5% agarose gel electrophoresis. The experiment comprised at least two biological replicates. Similar results were obtained in the two independent experiments. Data of one representative experiment are shown. (C) Quantification of VAR1 rRNA and 45S pre-rRNA in Arabidopsis 32E03-L line (14 and 18 d old) by qPCR. Wild-type plants were used as control. (D) Quantification of rRNA VAR1 and 45S pre-rRNA in wild-type Arabidopsis root segments enriched in H. schachtii -induced syncytia by qPCR. Wild-type plants were inoculated with H. schachtii J2s and root segments enriched in H. schachtii -induced syncytia (root+syncytium) and adjacent root segments without syncytia (root-syncytium; control) were dissected at 10 d postinoculation. In (C) and (D) , whole roots or root segments cDNA was synthesized, and VAR1 and 45S pre-RNA were quantified by qPCR. ACTIN8 was amplified as reference. The experiments comprised three biological replicates, each consisting of three technical replicates. Similar results were obtained in the three independent experiments. Data of one representative experiment are shown. For (A) to (D) , plants of the tested genotypes/treatments were grown in randomized block designs. For each biological replicate, plants were sampled randomly to prepare pools for each genotype/treatment.

    Techniques Used: Variant Assay, Expressing, Synthesized, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction, Blocking Assay

    31) Product Images from "Nickel and low CO2-controlled motility in Chlamydomonas through complementation of a paralyzed flagella mutant with chemically regulated promoters"

    Article Title: Nickel and low CO2-controlled motility in Chlamydomonas through complementation of a paralyzed flagella mutant with chemically regulated promoters

    Journal: BMC Plant Biology

    doi: 10.1186/1471-2229-11-22

    Constitutive complementation of the pf14 mutant by the PSAD:RSP3-HA construct . Panel A: Percentage of swimming (S), flagellated-immotile (F/I) and non-flagellated (NF) cells in a single, rescued transformant. Panel B: Western blotting of the PSAD:RSP3-HA transformant and pf14 mutant probed with the anti-HA antibody. M, molecular weight marker. Cells were grown in 24-well microtiter plates. For details, see Methods.
    Figure Legend Snippet: Constitutive complementation of the pf14 mutant by the PSAD:RSP3-HA construct . Panel A: Percentage of swimming (S), flagellated-immotile (F/I) and non-flagellated (NF) cells in a single, rescued transformant. Panel B: Western blotting of the PSAD:RSP3-HA transformant and pf14 mutant probed with the anti-HA antibody. M, molecular weight marker. Cells were grown in 24-well microtiter plates. For details, see Methods.

    Techniques Used: Mutagenesis, Construct, Western Blot, Molecular Weight, Marker

    32) Product Images from "Nickel and low CO2-controlled motility in Chlamydomonas through complementation of a paralyzed flagella mutant with chemically regulated promoters"

    Article Title: Nickel and low CO2-controlled motility in Chlamydomonas through complementation of a paralyzed flagella mutant with chemically regulated promoters

    Journal: BMC Plant Biology

    doi: 10.1186/1471-2229-11-22

    Constitutive complementation of the pf14 mutant by the PSAD:RSP3-HA construct . Panel A: Percentage of swimming (S), flagellated-immotile (F/I) and non-flagellated (NF) cells in a single, rescued transformant. Panel B: Western blotting of the PSAD:RSP3-HA transformant and pf14 mutant probed with the anti-HA antibody. M, molecular weight marker. Cells were grown in 24-well microtiter plates. For details, see Methods.
    Figure Legend Snippet: Constitutive complementation of the pf14 mutant by the PSAD:RSP3-HA construct . Panel A: Percentage of swimming (S), flagellated-immotile (F/I) and non-flagellated (NF) cells in a single, rescued transformant. Panel B: Western blotting of the PSAD:RSP3-HA transformant and pf14 mutant probed with the anti-HA antibody. M, molecular weight marker. Cells were grown in 24-well microtiter plates. For details, see Methods.

    Techniques Used: Mutagenesis, Construct, Western Blot, Molecular Weight, Marker

    Chemically inducible complementation of the pf14 mutant by the CYC6:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 48 hours after Ni addition. The transformants were grown in TAP ENEA2 medium in 24-well microtiter plates and induced at mid-log phase with 25 μM Ni. For details, see Methods.
    Figure Legend Snippet: Chemically inducible complementation of the pf14 mutant by the CYC6:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 48 hours after Ni addition. The transformants were grown in TAP ENEA2 medium in 24-well microtiter plates and induced at mid-log phase with 25 μM Ni. For details, see Methods.

    Techniques Used: Mutagenesis, Construct

    Chemically inducible complementation of the pf14 mutant by the CAH1:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 6 hours after induction by low CO 2 . The transformants were grown in minimal medium with extra phosphate in 24-well microtiter plates, under air containing 5% CO 2 , and induced at early log phase by shifting to air with no CO 2 supplementation. For details, see Methods.
    Figure Legend Snippet: Chemically inducible complementation of the pf14 mutant by the CAH1:RSP3-HA construct . Percentage of swimming (S) and flagellated-immotile (F/I) cells of two transformants, 6 hours after induction by low CO 2 . The transformants were grown in minimal medium with extra phosphate in 24-well microtiter plates, under air containing 5% CO 2 , and induced at early log phase by shifting to air with no CO 2 supplementation. For details, see Methods.

    Techniques Used: Mutagenesis, Construct

    33) Product Images from "SUVH1, a Su(var)3–9 family member, promotes the expression of genes targeted by DNA methylation"

    Article Title: SUVH1, a Su(var)3–9 family member, promotes the expression of genes targeted by DNA methylation

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv958

    The suvh1–1 mutation does not affect DNA methylation. ( A and B ) McrBC-qPCR analysis of DNA methylation levels at the d35S promoter and the LUC coding region in YJ (A) and LUCH (B). qPCR was performed using genomic DNA treated with or without McrBC. The relative levels of amplified DNA for UBQ5, LUC and d35S in samples treated with McrBC compared to untreated samples were shown. Error bars were from three technical replicates. Two biological replicates were performed and gave similar results. ( C and D ) The levels of CG, CHG and CHH DNA methylation at the d35S promoter (C) and LUC coding region (D) in YJ and YJ suvh1–1 as determined through MethylC sequencing. Results from two biological replicates (rep) are shown. (E) Total genomic CG, CHG and CHH DNA methylation in YJ and YJ suvh1–1 as determined through MethylC-seq. Results from two biological replicates (rep) are shown.
    Figure Legend Snippet: The suvh1–1 mutation does not affect DNA methylation. ( A and B ) McrBC-qPCR analysis of DNA methylation levels at the d35S promoter and the LUC coding region in YJ (A) and LUCH (B). qPCR was performed using genomic DNA treated with or without McrBC. The relative levels of amplified DNA for UBQ5, LUC and d35S in samples treated with McrBC compared to untreated samples were shown. Error bars were from three technical replicates. Two biological replicates were performed and gave similar results. ( C and D ) The levels of CG, CHG and CHH DNA methylation at the d35S promoter (C) and LUC coding region (D) in YJ and YJ suvh1–1 as determined through MethylC sequencing. Results from two biological replicates (rep) are shown. (E) Total genomic CG, CHG and CHH DNA methylation in YJ and YJ suvh1–1 as determined through MethylC-seq. Results from two biological replicates (rep) are shown.

    Techniques Used: Mutagenesis, DNA Methylation Assay, Real-time Polymerase Chain Reaction, Amplification, Sequencing

    Plots of DNA methylation levels at 1 kb gene promoter regions versus gene expression levels in YJ and YJ suvh1–1 . The x-axis represents the level of DNA methylation, and the y-axis represents the natural logarithm of the RPKM (reads per kilobase per million) value for genes from mRNA-seq. ( A and B ) Correlation plot of CG methylation level with gene expression in YJ (A) and YJ suvh1–1 (B). ( C and D ) Correlation plot of CHG methylation level with gene expression in YJ (C) and YJ suvh1–1 (D). ( E and F ) Correlation plot of CHH methylation level with gene expression in YJ (E) and YJ suvh1–1 (F) DNA methylation and gene expression levels were determined from MethylC-seq and mRNA-seq, respectively, in this study.
    Figure Legend Snippet: Plots of DNA methylation levels at 1 kb gene promoter regions versus gene expression levels in YJ and YJ suvh1–1 . The x-axis represents the level of DNA methylation, and the y-axis represents the natural logarithm of the RPKM (reads per kilobase per million) value for genes from mRNA-seq. ( A and B ) Correlation plot of CG methylation level with gene expression in YJ (A) and YJ suvh1–1 (B). ( C and D ) Correlation plot of CHG methylation level with gene expression in YJ (C) and YJ suvh1–1 (D). ( E and F ) Correlation plot of CHH methylation level with gene expression in YJ (E) and YJ suvh1–1 (F) DNA methylation and gene expression levels were determined from MethylC-seq and mRNA-seq, respectively, in this study.

    Techniques Used: DNA Methylation Assay, Expressing, Methylation

    34) Product Images from "Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring"

    Article Title: Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring

    Journal: BMC Genomics

    doi: 10.1186/s12864-018-4813-8

    Whole-genome dot-plot comparison of six Populus cpDNAs. The chloroplast genomes of all six Populus species, P. alba , P. tremula , P. euphratica , P. fremontii , P. balsamifera and P. trichocarpa , were compared using LASTZ (v1.03.28). The aligned blocks are represented as blue lines. The blocks aligned in the reverse orientation are a pair of inverted repeats (IRa IRb) in the chloroplast genomes. The starts and ends of the aligned blocks are labeled with transparent red points
    Figure Legend Snippet: Whole-genome dot-plot comparison of six Populus cpDNAs. The chloroplast genomes of all six Populus species, P. alba , P. tremula , P. euphratica , P. fremontii , P. balsamifera and P. trichocarpa , were compared using LASTZ (v1.03.28). The aligned blocks are represented as blue lines. The blocks aligned in the reverse orientation are a pair of inverted repeats (IRa IRb) in the chloroplast genomes. The starts and ends of the aligned blocks are labeled with transparent red points

    Techniques Used: Labeling

    35) Product Images from "Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana"

    Article Title: Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

    Journal: BMC Genomics

    doi: 10.1186/s12864-018-4878-4

    Frequency distributions of different types of SSR repeat units in Nicotiana genomes. N. ben, N. syl, N. tom, N. oto, N. tab TN90, K326 and BX represent N. benthamiana , N. sylvestris , N. tomentosiformis , N. otophora , N. tabacum TN90, N. tabacum K326, and N. tabacum BX, respectively
    Figure Legend Snippet: Frequency distributions of different types of SSR repeat units in Nicotiana genomes. N. ben, N. syl, N. tom, N. oto, N. tab TN90, K326 and BX represent N. benthamiana , N. sylvestris , N. tomentosiformis , N. otophora , N. tabacum TN90, N. tabacum K326, and N. tabacum BX, respectively

    Techniques Used:

    Experimental validations of NIX markers by amplification and allele scoring. Image shows the PCR fragments resolved by agarose gel ( a ) or DNA fragment analyzer ABI3730X ( b ). N. syl, N. tom, N. Tab HD, N. Tab K326, and N. ben represent N. sylvestris, N. tomentosiformis , N. tabacum HD, N. tabacum K326 (K), and N. benthamiana (B) , respectively. The numbers in the image represent validated IDs for markers
    Figure Legend Snippet: Experimental validations of NIX markers by amplification and allele scoring. Image shows the PCR fragments resolved by agarose gel ( a ) or DNA fragment analyzer ABI3730X ( b ). N. syl, N. tom, N. Tab HD, N. Tab K326, and N. ben represent N. sylvestris, N. tomentosiformis , N. tabacum HD, N. tabacum K326 (K), and N. benthamiana (B) , respectively. The numbers in the image represent validated IDs for markers

    Techniques Used: Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis

    36) Product Images from "Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed"

    Article Title: Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed

    Journal: Nature Communications

    doi: 10.1038/s41467-019-13927-3

    Promoter CHH methylation and expression of IAA27 differ between CLSY1 allelic variants. Average DNA methylation rates in CHH, CHG and CG context and average IAA27 mRNA abundance in n = 10 accessions carrying the CLSY1 D-allele (D) and n = 10 accessions carrying the CLSY1 E-allele (E). Cytosine methylation was determined over an upstream region of IAA27 (chr04:14327600-14329000 bp, Col-0 genome, TAIR10). IAA27 transcript levels were determined relative to PP2A using qRT-PCR on roots from three independent experiments per genotype with 18 roots per experiment pooled for RNA extraction. ***: significant difference at P
    Figure Legend Snippet: Promoter CHH methylation and expression of IAA27 differ between CLSY1 allelic variants. Average DNA methylation rates in CHH, CHG and CG context and average IAA27 mRNA abundance in n = 10 accessions carrying the CLSY1 D-allele (D) and n = 10 accessions carrying the CLSY1 E-allele (E). Cytosine methylation was determined over an upstream region of IAA27 (chr04:14327600-14329000 bp, Col-0 genome, TAIR10). IAA27 transcript levels were determined relative to PP2A using qRT-PCR on roots from three independent experiments per genotype with 18 roots per experiment pooled for RNA extraction. ***: significant difference at P

    Techniques Used: Methylation, Expressing, DNA Methylation Assay, Quantitative RT-PCR, RNA Extraction

    37) Product Images from "Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species"

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species

    Journal:

    doi:

    Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;
    Figure Legend Snippet: Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;

    Techniques Used: DNA Extraction, Infection, Polymerase Chain Reaction

    38) Product Images from "Isolation of nucleic acids using silicon dioxide powder as a tool for environmental monitoring"

    Article Title: Isolation of nucleic acids using silicon dioxide powder as a tool for environmental monitoring

    Journal: Environmental Monitoring and Assessment

    doi: 10.1007/s10661-019-7840-2

    a DNA isolate evaluation - silica dioxide powder, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder. Samples 7b–10b were amplificated twice; b DNA isolate evaluation -NucleoSpin® Plant II/Macherey Nagel Kit, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder; c DNA isolate evaluation -DNeasy Plant Mini Kit/Qiagen, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder; d DNA isolate evaluation-CTAB method, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder.
    Figure Legend Snippet: a DNA isolate evaluation - silica dioxide powder, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder. Samples 7b–10b were amplificated twice; b DNA isolate evaluation -NucleoSpin® Plant II/Macherey Nagel Kit, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder; c DNA isolate evaluation -DNeasy Plant Mini Kit/Qiagen, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder; d DNA isolate evaluation-CTAB method, PCR amplification of the ITS region. For sample details, see Table 2 . Lane M, 100 bp DNA ladder.

    Techniques Used: Polymerase Chain Reaction, Amplification

    39) Product Images from "The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status"

    Article Title: The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

    Journal: eLife

    doi: 10.7554/eLife.19893

    Investigation of transgene copy number. ( A ) Diagram of the At1g02740 gene showing the location of the YJ reporter insertion site based on the MethylC-seq reads. Chimeric reads between the YJ reporter, in the vicinity of the RB and LB elements, mapped exclusively to the At1g02740 3’UTR and are shown above the At1g02740 gene. A deletion in the At1g02740 3’UTR inferred from these same sequences is shown below the At1g02740 gene. ( B ) Genome browser view showing the results from mapping the MethylC-seq data to the entire binary vector used for the generation of the YJ reporter line. The individual reads are shown in grey (lower track) and the total read coverage in purple (upper track). Negligible reads were identified mapping to the plasmid backbone. ( C ) Model showing a single copy insertion of the YJ reporter into the At1g02740 3’UTR . ( D ) Diagram of the At3g07350 gene showing the location of the LUCH reporter insertion site based on the MethylC-seq reads. Chimeric reads between the LUCH reporter, in the vicinity of the RB and LB elements, mapped to several genetic elements. (1) Chimeric reads corresponding to the outermost regions of the insert mapped to the coding sequence of the At3g07350 gene and are shown above the gene model. A deletion in the At3g07350 coding sequence inferred from the MethylC-seq data is shown below the At3g07350 gene. (2) Reads mapping to the LUCH reporter that extend beyond the RB into the plasmid backbone were also identified. (3) Finally, chimeric reads consistent with the presence of an LUCH inverted repeat, were also present. ( E ) Genome browser view showing the coverage results from mapping the MethylC-seq data to the binary vector used for the generation of the LUCH reporter line. Reads spanning nearly the entire plasmid backbone were identified suggesting a non-canonical insertion profile. ( F ) Model of one possible configuration of the LUCH reporter that is consistent with the junctions identified in panel ( D ), the presence of the entire binary vector as identified in panel ( E ), and published Southern blot data ( Won et al., 2012 ). The colors of the sequences and elements are as indicated. Sequences in capital or lower case represent coding and non-coding sequences, respectively. The bold, italic purple sequence in panel ( D ) demarcates the inverted repeat in the vicinity of the LUCH LB. In panel ( E ), the read numbers are capped at 50 and regions with > 50 reads are indicated by the presence of a thick black bar above the reads. DOI: http://dx.doi.org/10.7554/eLife.19893.005
    Figure Legend Snippet: Investigation of transgene copy number. ( A ) Diagram of the At1g02740 gene showing the location of the YJ reporter insertion site based on the MethylC-seq reads. Chimeric reads between the YJ reporter, in the vicinity of the RB and LB elements, mapped exclusively to the At1g02740 3’UTR and are shown above the At1g02740 gene. A deletion in the At1g02740 3’UTR inferred from these same sequences is shown below the At1g02740 gene. ( B ) Genome browser view showing the results from mapping the MethylC-seq data to the entire binary vector used for the generation of the YJ reporter line. The individual reads are shown in grey (lower track) and the total read coverage in purple (upper track). Negligible reads were identified mapping to the plasmid backbone. ( C ) Model showing a single copy insertion of the YJ reporter into the At1g02740 3’UTR . ( D ) Diagram of the At3g07350 gene showing the location of the LUCH reporter insertion site based on the MethylC-seq reads. Chimeric reads between the LUCH reporter, in the vicinity of the RB and LB elements, mapped to several genetic elements. (1) Chimeric reads corresponding to the outermost regions of the insert mapped to the coding sequence of the At3g07350 gene and are shown above the gene model. A deletion in the At3g07350 coding sequence inferred from the MethylC-seq data is shown below the At3g07350 gene. (2) Reads mapping to the LUCH reporter that extend beyond the RB into the plasmid backbone were also identified. (3) Finally, chimeric reads consistent with the presence of an LUCH inverted repeat, were also present. ( E ) Genome browser view showing the coverage results from mapping the MethylC-seq data to the binary vector used for the generation of the LUCH reporter line. Reads spanning nearly the entire plasmid backbone were identified suggesting a non-canonical insertion profile. ( F ) Model of one possible configuration of the LUCH reporter that is consistent with the junctions identified in panel ( D ), the presence of the entire binary vector as identified in panel ( E ), and published Southern blot data ( Won et al., 2012 ). The colors of the sequences and elements are as indicated. Sequences in capital or lower case represent coding and non-coding sequences, respectively. The bold, italic purple sequence in panel ( D ) demarcates the inverted repeat in the vicinity of the LUCH LB. In panel ( E ), the read numbers are capped at 50 and regions with > 50 reads are indicated by the presence of a thick black bar above the reads. DOI: http://dx.doi.org/10.7554/eLife.19893.005

    Techniques Used: Plasmid Preparation, Sequencing, Southern Blot

    40) Product Images from "The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status"

    Article Title: The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

    Journal: eLife

    doi: 10.7554/eLife.19893

    Investigation of transgene copy number. ( A ) Diagram of the At1g02740 gene showing the location of the YJ reporter insertion site based on the MethylC-seq reads. Chimeric reads between the YJ reporter, in the vicinity of the RB and LB elements, mapped exclusively to the At1g02740 3’UTR and are shown above the At1g02740 gene. A deletion in the At1g02740 3’UTR inferred from these same sequences is shown below the At1g02740 gene. ( B ) Genome browser view showing the results from mapping the MethylC-seq data to the entire binary vector used for the generation of the YJ reporter line. The individual reads are shown in grey (lower track) and the total read coverage in purple (upper track). Negligible reads were identified mapping to the plasmid backbone. ( C ) Model showing a single copy insertion of the YJ reporter into the At1g02740 3’UTR . ( D ) Diagram of the At3g07350 gene showing the location of the LUCH reporter insertion site based on the MethylC-seq reads. Chimeric reads between the LUCH reporter, in the vicinity of the RB and LB elements, mapped to several genetic elements. (1) Chimeric reads corresponding to the outermost regions of the insert mapped to the coding sequence of the At3g07350 gene and are shown above the gene model. A deletion in the At3g07350 coding sequence inferred from the MethylC-seq data is shown below the At3g07350 gene. (2) Reads mapping to the LUCH reporter that extend beyond the RB into the plasmid backbone were also identified. (3) Finally, chimeric reads consistent with the presence of an LUCH inverted repeat, were also present. ( E ) Genome browser view showing the coverage results from mapping the MethylC-seq data to the binary vector used for the generation of the LUCH reporter line. Reads spanning nearly the entire plasmid backbone were identified suggesting a non-canonical insertion profile. ( F ) Model of one possible configuration of the LUCH reporter that is consistent with the junctions identified in panel ( D ), the presence of the entire binary vector as identified in panel ( E ), and published Southern blot data ( Won et al., 2012 ). The colors of the sequences and elements are as indicated. Sequences in capital or lower case represent coding and non-coding sequences, respectively. The bold, italic purple sequence in panel ( D ) demarcates the inverted repeat in the vicinity of the LUCH LB. In panel ( E ), the read numbers are capped at 50 and regions with > 50 reads are indicated by the presence of a thick black bar above the reads. DOI: http://dx.doi.org/10.7554/eLife.19893.005
    Figure Legend Snippet: Investigation of transgene copy number. ( A ) Diagram of the At1g02740 gene showing the location of the YJ reporter insertion site based on the MethylC-seq reads. Chimeric reads between the YJ reporter, in the vicinity of the RB and LB elements, mapped exclusively to the At1g02740 3’UTR and are shown above the At1g02740 gene. A deletion in the At1g02740 3’UTR inferred from these same sequences is shown below the At1g02740 gene. ( B ) Genome browser view showing the results from mapping the MethylC-seq data to the entire binary vector used for the generation of the YJ reporter line. The individual reads are shown in grey (lower track) and the total read coverage in purple (upper track). Negligible reads were identified mapping to the plasmid backbone. ( C ) Model showing a single copy insertion of the YJ reporter into the At1g02740 3’UTR . ( D ) Diagram of the At3g07350 gene showing the location of the LUCH reporter insertion site based on the MethylC-seq reads. Chimeric reads between the LUCH reporter, in the vicinity of the RB and LB elements, mapped to several genetic elements. (1) Chimeric reads corresponding to the outermost regions of the insert mapped to the coding sequence of the At3g07350 gene and are shown above the gene model. A deletion in the At3g07350 coding sequence inferred from the MethylC-seq data is shown below the At3g07350 gene. (2) Reads mapping to the LUCH reporter that extend beyond the RB into the plasmid backbone were also identified. (3) Finally, chimeric reads consistent with the presence of an LUCH inverted repeat, were also present. ( E ) Genome browser view showing the coverage results from mapping the MethylC-seq data to the binary vector used for the generation of the LUCH reporter line. Reads spanning nearly the entire plasmid backbone were identified suggesting a non-canonical insertion profile. ( F ) Model of one possible configuration of the LUCH reporter that is consistent with the junctions identified in panel ( D ), the presence of the entire binary vector as identified in panel ( E ), and published Southern blot data ( Won et al., 2012 ). The colors of the sequences and elements are as indicated. Sequences in capital or lower case represent coding and non-coding sequences, respectively. The bold, italic purple sequence in panel ( D ) demarcates the inverted repeat in the vicinity of the LUCH LB. In panel ( E ), the read numbers are capped at 50 and regions with > 50 reads are indicated by the presence of a thick black bar above the reads. DOI: http://dx.doi.org/10.7554/eLife.19893.005

    Techniques Used: Plasmid Preparation, Sequencing, Southern Blot

    Related Articles

    DNA Extraction:

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. Three leaf disks were used for DNA extraction using the DNeasy Plant Mini Kit (Qiagen, Inc.), and the final three leaf disks were subjected to NaOH lysis. .. For the NaOH extraction method, the three leaf disks were briefly ground for 5 to 10 sec in 150 μl of 0.5N NaOH using a polypropylene Pellet Pestle (Kimble/Kontes, Vineland, NJ) to disrupt the cells, after which 5 μl was transferred immediately into a sterile 1.5 ml microcentrifuge tube containing 495 μl of 100 mM Tris-HCl, pH 8.3 ( ).

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. While the NaOH lysis protocol for DNA extraction has not been tested as extensively as the Qiagen Dneasy Plant Mini Kit for sensitivity and reproducibility, implementation would greatly reduce both the overall cost of our PCR-based assay and the time required to perform the assay. .. The relative efficiency of foliar nematode detection using our PCR-based assay was significantly higher compared to conventional water extraction when assaying asymptomatic plant tissue.

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. NaOH-based DNA extraction from A. fragariae -infected Salvia plants produced successful PCR products with the AFragFl and AFragRl primers, while DNA extracted from infected Salvia tissue using the Qiagen Dneasy Plant Mini Kit did not. .. While the NaOH lysis protocol for DNA extraction has not been tested as extensively as the Qiagen Dneasy Plant Mini Kit for sensitivity and reproducibility, implementation would greatly reduce both the overall cost of our PCR-based assay and the time required to perform the assay.

    Article Title: Promoting the accumulation of scopolamine and hyoscyamine in Hyoscyamus niger L. through EMS based mutagenesis
    Article Snippet: .. Total genomic DNA was extracted from control and EMS treated samples using a DNA isolation kit (DNeasy- Plant Mini kit-Qiagen, Germany). .. The extracted DNA was quantified by Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

    Amplification:

    Article Title: Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress
    Article Snippet: .. Transgenes for Arabidopsis experiments FLOE1’s genomic region spanning its promoter, as predicted by AGRIS , to its last coding codon was amplified by Phusion (Thermo Fisher Scientific) PCR from Col-0 DNA (extracted with DNeasy Plant Mini Kit (Qiagen)) using the prigFLOE1-FWD/REV primers (Table S3). .. The amplicon was first cloned into pDONR221 (Thermo Fisher Scientific) using BP Clonase II (Thermo Fisher Scientific) and then subcloned into pGWB604, pGWB610 and pGWB633using LR Clonase II (Thermo Fisher Scientific) to generate pFLOE1p:FLOE1-GFP, pFLOE1p:FLOE1-FLAG and pFLOE1p:FLOE1-GUS respectively. pFLOE1p:FLOE1ΔDS-GFP, pFLOE1p:FLOE1ΔQPS-GFP, and pFLOE1p:FLOE1ΔDUF-GFP were obtained by modifying pFLOE1p:FLOE1-GFP using the Q5 Site-Directed Mutagenesis Kit (New England Biolabs) with primers priDSdeletion-FWD/REV, priQPSdeletion-FWD/REV, and priDUFdeletion-FWD/REV (Table S3) respectively.

    Infection:

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. NaOH-based DNA extraction from A. fragariae -infected Salvia plants produced successful PCR products with the AFragFl and AFragRl primers, while DNA extracted from infected Salvia tissue using the Qiagen Dneasy Plant Mini Kit did not. .. While the NaOH lysis protocol for DNA extraction has not been tested as extensively as the Qiagen Dneasy Plant Mini Kit for sensitivity and reproducibility, implementation would greatly reduce both the overall cost of our PCR-based assay and the time required to perform the assay.

    Produced:

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. NaOH-based DNA extraction from A. fragariae -infected Salvia plants produced successful PCR products with the AFragFl and AFragRl primers, while DNA extracted from infected Salvia tissue using the Qiagen Dneasy Plant Mini Kit did not. .. While the NaOH lysis protocol for DNA extraction has not been tested as extensively as the Qiagen Dneasy Plant Mini Kit for sensitivity and reproducibility, implementation would greatly reduce both the overall cost of our PCR-based assay and the time required to perform the assay.

    Polymerase Chain Reaction:

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. While the NaOH lysis protocol for DNA extraction has not been tested as extensively as the Qiagen Dneasy Plant Mini Kit for sensitivity and reproducibility, implementation would greatly reduce both the overall cost of our PCR-based assay and the time required to perform the assay. .. The relative efficiency of foliar nematode detection using our PCR-based assay was significantly higher compared to conventional water extraction when assaying asymptomatic plant tissue.

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. NaOH-based DNA extraction from A. fragariae -infected Salvia plants produced successful PCR products with the AFragFl and AFragRl primers, while DNA extracted from infected Salvia tissue using the Qiagen Dneasy Plant Mini Kit did not. .. While the NaOH lysis protocol for DNA extraction has not been tested as extensively as the Qiagen Dneasy Plant Mini Kit for sensitivity and reproducibility, implementation would greatly reduce both the overall cost of our PCR-based assay and the time required to perform the assay.

    Article Title: Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress
    Article Snippet: .. Transgenes for Arabidopsis experiments FLOE1’s genomic region spanning its promoter, as predicted by AGRIS , to its last coding codon was amplified by Phusion (Thermo Fisher Scientific) PCR from Col-0 DNA (extracted with DNeasy Plant Mini Kit (Qiagen)) using the prigFLOE1-FWD/REV primers (Table S3). .. The amplicon was first cloned into pDONR221 (Thermo Fisher Scientific) using BP Clonase II (Thermo Fisher Scientific) and then subcloned into pGWB604, pGWB610 and pGWB633using LR Clonase II (Thermo Fisher Scientific) to generate pFLOE1p:FLOE1-GFP, pFLOE1p:FLOE1-FLAG and pFLOE1p:FLOE1-GUS respectively. pFLOE1p:FLOE1ΔDS-GFP, pFLOE1p:FLOE1ΔQPS-GFP, and pFLOE1p:FLOE1ΔDUF-GFP were obtained by modifying pFLOE1p:FLOE1-GFP using the Q5 Site-Directed Mutagenesis Kit (New England Biolabs) with primers priDSdeletion-FWD/REV, priQPSdeletion-FWD/REV, and priDUFdeletion-FWD/REV (Table S3) respectively.

    Incubation:

    Article Title: In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes
    Article Snippet: .. The homogenates were further processed using modified steps from the standard protocols developed for the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and MoBio Power Plant Kit (MoBio, Carlsbad, CA, USA), as specified: Method # 1 (M1)—modified method based on the Qiagen DNeasy Plant Mini Kit: following sample disruption using the Mini-Beadbeater-24, samples were incubated at 75 °C for 10 min, instead of 65 °C as recommended by the manufacturer, mixing the sample thoroughly every 2 min using a vortex. .. In addition, samples were incubated for an additional 5 min, with an intense final mixing at the end of the 5 min (step 2, Quick Start protocol, Qiagen).

    Modification:

    Article Title: In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes
    Article Snippet: .. The homogenates were further processed using modified steps from the standard protocols developed for the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and MoBio Power Plant Kit (MoBio, Carlsbad, CA, USA), as specified: Method # 1 (M1)—modified method based on the Qiagen DNeasy Plant Mini Kit: following sample disruption using the Mini-Beadbeater-24, samples were incubated at 75 °C for 10 min, instead of 65 °C as recommended by the manufacturer, mixing the sample thoroughly every 2 min using a vortex. .. In addition, samples were incubated for an additional 5 min, with an intense final mixing at the end of the 5 min (step 2, Quick Start protocol, Qiagen).

    Lysis:

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. Three leaf disks were used for DNA extraction using the DNeasy Plant Mini Kit (Qiagen, Inc.), and the final three leaf disks were subjected to NaOH lysis. .. For the NaOH extraction method, the three leaf disks were briefly ground for 5 to 10 sec in 150 μl of 0.5N NaOH using a polypropylene Pellet Pestle (Kimble/Kontes, Vineland, NJ) to disrupt the cells, after which 5 μl was transferred immediately into a sterile 1.5 ml microcentrifuge tube containing 495 μl of 100 mM Tris-HCl, pH 8.3 ( ).

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species
    Article Snippet: .. While the NaOH lysis protocol for DNA extraction has not been tested as extensively as the Qiagen Dneasy Plant Mini Kit for sensitivity and reproducibility, implementation would greatly reduce both the overall cost of our PCR-based assay and the time required to perform the assay. .. The relative efficiency of foliar nematode detection using our PCR-based assay was significantly higher compared to conventional water extraction when assaying asymptomatic plant tissue.

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    Qiagen dna isolation kit
    Representative image of <t>DNA</t> extraction and PCR analysis of H6H and PMT gene isolated from <t>EMS</t> treated and control explants of H . niger of different samples (500 and 400bp respectively) of (A) DNA extraction isolated from explants treated with different concentrations of EMS and untreated. (B) Depicts the PCR analysis of H6H (500bp) Gene (C) PCR amplification PMT Gene (400bp).
    Dna Isolation Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 2654 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Representative image of DNA extraction and PCR analysis of H6H and PMT gene isolated from EMS treated and control explants of H . niger of different samples (500 and 400bp respectively) of (A) DNA extraction isolated from explants treated with different concentrations of EMS and untreated. (B) Depicts the PCR analysis of H6H (500bp) Gene (C) PCR amplification PMT Gene (400bp).

    Journal: PLoS ONE

    Article Title: Promoting the accumulation of scopolamine and hyoscyamine in Hyoscyamus niger L. through EMS based mutagenesis

    doi: 10.1371/journal.pone.0231355

    Figure Lengend Snippet: Representative image of DNA extraction and PCR analysis of H6H and PMT gene isolated from EMS treated and control explants of H . niger of different samples (500 and 400bp respectively) of (A) DNA extraction isolated from explants treated with different concentrations of EMS and untreated. (B) Depicts the PCR analysis of H6H (500bp) Gene (C) PCR amplification PMT Gene (400bp).

    Article Snippet: Total genomic DNA was extracted from control and EMS treated samples using a DNA isolation kit (DNeasy- Plant Mini kit-Qiagen, Germany).

    Techniques: DNA Extraction, Polymerase Chain Reaction, Isolation, Amplification

    Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;

    Journal:

    Article Title: Conventional and PCR Detection of Aphelenchoides fragariae in Diverse Ornamental Host Plant Species

    doi:

    Figure Lengend Snippet: Comparison of DNA extraction methods for detection of Aphelenchoides fragariae in naturally infected Asplenium nidus (Bird's nest fern) plant tissue using species-specific PCR primers. Lane 1: healthy A. nidus extracted with Qiagen Dneasy Plant Mini Kit;

    Article Snippet: Increasing increments of nematodes from 1 to 1,000 were hand picked and combined with three non-infected A. nidus leaf disks, and total DNA was extracted using the Qiagen DNeasy Plant Mini Kit.

    Techniques: DNA Extraction, Infection, Polymerase Chain Reaction

    Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.

    Journal: Plants

    Article Title: In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes

    doi: 10.3390/plants6040052

    Figure Lengend Snippet: Schematic design of the methods adapted to extract genomic DNA from light or dark-adapted pin oak ( Q. palustris ) leaves or leaves of other species rich in polysaccharides and secondary metabolites: ( a ) M1, using CTAB (based on Qiagen DNeasy Plant DNA extraction kit) and ( b ) M2, using phenol (based on MoBio Power Plant DNA extraction kit) for contaminant removal. Red box framing indicates steps specifically modified within this work, differing from kit manufacturer recommendations.

    Article Snippet: The homogenates were further processed using modified steps from the standard protocols developed for the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and MoBio Power Plant Kit (MoBio, Carlsbad, CA, USA), as specified: Method # 1 (M1)—modified method based on the Qiagen DNeasy Plant Mini Kit: following sample disruption using the Mini-Beadbeater-24, samples were incubated at 75 °C for 10 min, instead of 65 °C as recommended by the manufacturer, mixing the sample thoroughly every 2 min using a vortex.

    Techniques: DNA Extraction, Modification