genomic dna  (Zymo Research)


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    Name:
    Genomic DNA Wash 1
    Description:

    Catalog Number:
    d3067-2-25
    Price:
    None
    Category:
    Life Science Reagents and Media
    Applications:
    DNA Purification
    Size:
    25 ml
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    Structured Review

    Zymo Research genomic dna
    Genomic DNA Wash 1

    https://www.bioz.com/result/genomic dna/product/Zymo Research
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    genomic dna - by Bioz Stars, 2021-03
    86/100 stars

    Images

    1) Product Images from "Global DNA Hypomethylation and Rassf1a and c-myc Promoter Hypermethylation in Rat Kidney Cells after Bisphenol A Exposure"

    Article Title: Global DNA Hypomethylation and Rassf1a and c-myc Promoter Hypermethylation in Rat Kidney Cells after Bisphenol A Exposure

    Journal: Turkish Journal of Pharmaceutical Sciences

    doi: 10.4274/tjps.galenos.2019.57983

    Effects of BPA on methylation status of c-myc in NRK-52E cells. A representative sample of NRK-52E cells treated with BPA at the concentrations of 1 nM, 10 nM, 100 nM, 1 μM, and 10 μM for 24 h and concentration of 100 nM for 24, 48, 72, 96 h, and 6 days is shown. Methylation was determined by bisulfite modification of the genomic DNA and MSP using primers for the U or M promoter sequence. C1 and C2=DMSO (1%) as control instead of BPA treatment U: Unmethylated, M: Methylated, BPA: Bisphenol A, MSP: Methylation specific, DMSO: Dimethyl sulfoxide, C1: Contol 1, C2: Control 2
    Figure Legend Snippet: Effects of BPA on methylation status of c-myc in NRK-52E cells. A representative sample of NRK-52E cells treated with BPA at the concentrations of 1 nM, 10 nM, 100 nM, 1 μM, and 10 μM for 24 h and concentration of 100 nM for 24, 48, 72, 96 h, and 6 days is shown. Methylation was determined by bisulfite modification of the genomic DNA and MSP using primers for the U or M promoter sequence. C1 and C2=DMSO (1%) as control instead of BPA treatment U: Unmethylated, M: Methylated, BPA: Bisphenol A, MSP: Methylation specific, DMSO: Dimethyl sulfoxide, C1: Contol 1, C2: Control 2

    Techniques Used: Methylation, Concentration Assay, Modification, Sequencing

    Related Articles

    Methylation:

    Article Title: Aberrant DNA methylation and expression of SPDEF and FOXA2 in airway epithelium of patients with COPD
    Article Snippet: .. Methylation analysis by pyrosequencing For DNA methylation analysis of the target regions, genomic DNA was extracted with chloroform-isopropanol and bisulfite converted using the EZ DNA Methylation-Kit (Zymo Research), following the manufacturer’s protocol. .. Bisulfite-converted DNA (10–20 ng) was amplified by PCR in a 25 μl reaction using the Pyromark PCR kit (Qiagen).

    Article Title: Identification and validation of candidate epigenetic biomarkers in lung adenocarcinoma
    Article Snippet: DNA concentrations were measured using a NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). .. For MS-HRM analysis, 500 ng genomic DNA from each sample was subjected to sodium bisulfite treatment using the EZ-96 DNA Methylation-Gold™ kit (Zymo Research, Irvine, USA) according to the manufacturer´s instructions and eluted in a final volume of 52 μl. .. Microarray Analyses The microarray based screening for differentially methylated regions (DMRs) was performed as previously described .

    Article Title: Epigenetic Control of the Vasopressin Promoter Explains Physiological Ability to Regulate Vasopressin Transcription in Dehydration and Salt Loading States in the Rat
    Article Snippet: The concentrations of DNA and RNA were determined using a NanoDrop (Thermo Scientific, Waltham, MA, USA). .. Bisulphite conversion of DNA and TA cloning Genomic DNA from SON and cortex punches (50 ng) and rat hypothalamic 4B cells (200 ng) was bisulphite converted using EZ DNA Methylation‐Gold kit (Zymo Research). .. Primers for amplification of bisulphite converted DNA were designed using methprimer .

    DNA Methylation Assay:

    Article Title: Aberrant DNA methylation and expression of SPDEF and FOXA2 in airway epithelium of patients with COPD
    Article Snippet: .. Methylation analysis by pyrosequencing For DNA methylation analysis of the target regions, genomic DNA was extracted with chloroform-isopropanol and bisulfite converted using the EZ DNA Methylation-Kit (Zymo Research), following the manufacturer’s protocol. .. Bisulfite-converted DNA (10–20 ng) was amplified by PCR in a 25 μl reaction using the Pyromark PCR kit (Qiagen).

    Article Title: Reduced rRNA expression and increased rDNA promoter methylation in CD34+ cells of patients with myelodysplastic syndromes
    Article Snippet: The RT-PCR primers used were: pre-rRNA: forward primer 5′-gaacggtggtgtgtcgttc-3′, reverse primer 5′-gcgtctcgtctcgtctcact-3′; GAPDH: forward primer 5′-ccccttcattgacctcaactacat-3′, reverse primer 5′-cgctcctggaagatggtga-3′. .. Genomic DNA from CD34+ cells from 14 MDS samples and 11 normal samples (100-200 ng) and from myeloid cell lines (1 mg) was treated with sodium bisulfite using the EZ DNA methylation kit (Zymo Research). .. For 13 of 14 MDS samples and 8 of 11 control samples used for promoter methylation analysis, pre-rRNA expression was also studied by quantitative RT-PCR.

    Purification:

    Article Title: The Chromosome-Encoded Hypothetical Protein TC0668 Is an Upper Genital Tract Pathogenicity Factor of Chlamydia muridarum
    Article Snippet: The population frequencies of tc0237 and tc0668 nucleotide mutations were estimated using Sanger sequencing and subsequent signal analysis in MATLAB. .. Genomic DNA was purified from Nigg3 passaged whole-cell lysate with a Quick-gDNA MiniPrep kit (Zymo Research) according to the manufacturer's instructions. .. The coding regions of tc0237 and tc0668 were PCR amplified with KOD Hot Start master mix (EMD Millipore) and Sanger sequenced (ABI 3130XL operated by the UTHSCSA Nucleic Acids Core Facility) with a single read to cover known SNPs.

    Article Title: Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppression
    Article Snippet: Reduced Representation Bisulfite sequencing (RRBS-seq) For RRBS-seq analysis, Chr4-cl WT and KO ES cells were grown in either standard ES cell media containing FCS or for one week in 2i media containing vitamin C as described previously ( ). .. Genomic DNA was purified from WT and Chr4-cl KO ES cells using the Quick-gDNA purification kit (Zymo Research) and bisulfite-converted with the NEXTflex™ Bisulfite-Seq Kit (Bio Scientific) using Msp1 digestion to fragment DNA. ..

    Isolation:

    Article Title: A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2′-dC upon inhibition of ribonucleotide reductase
    Article Snippet: 3H decitabine incorporationThis assay was analogous to the reactivation treatment assays with a few modifications: assays were scaled 2.5-fold to 6-well format, 1 μl (1 μCi) of tritiated 5-aza-2′-dC (3H-Decitabine, Moravek Biochemicals Inc.) was added instead of cold 5-aza-2′-dC, and samples were harvested after 48 h of incubation. .. Cells were trypsinized, genomic DNA isolated using the Quick-gDNA MinPrep kit (Zymo Research), and measured by QuBit fluorometer (Life Technologies). .. Tritium content of 25 μl of genomic DNA was measured using a scintillation counter and normalized to the measured DNA concentration.

    Article Title: MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions
    Article Snippet: The PCR products is 327 bp for the mutant allele. .. Mass spec on gDNA Genomic DNA was extracted from isolated nuclei and fully digested with DNA Degradase Plus (Zymo Research). .. Samples were analyzed by mass spectrometry to quantify the amount of 5mCytosine and 5hmCytosine relative to Guanosine.

    Mass Spectrometry:

    Article Title: Identification and validation of candidate epigenetic biomarkers in lung adenocarcinoma
    Article Snippet: DNA concentrations were measured using a NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). .. For MS-HRM analysis, 500 ng genomic DNA from each sample was subjected to sodium bisulfite treatment using the EZ-96 DNA Methylation-Gold™ kit (Zymo Research, Irvine, USA) according to the manufacturer´s instructions and eluted in a final volume of 52 μl. .. Microarray Analyses The microarray based screening for differentially methylated regions (DMRs) was performed as previously described .

    Article Title: MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions
    Article Snippet: The PCR products is 327 bp for the mutant allele. .. Mass spec on gDNA Genomic DNA was extracted from isolated nuclei and fully digested with DNA Degradase Plus (Zymo Research). .. Samples were analyzed by mass spectrometry to quantify the amount of 5mCytosine and 5hmCytosine relative to Guanosine.

    TA Cloning:

    Article Title: Epigenetic Control of the Vasopressin Promoter Explains Physiological Ability to Regulate Vasopressin Transcription in Dehydration and Salt Loading States in the Rat
    Article Snippet: The concentrations of DNA and RNA were determined using a NanoDrop (Thermo Scientific, Waltham, MA, USA). .. Bisulphite conversion of DNA and TA cloning Genomic DNA from SON and cortex punches (50 ng) and rat hypothalamic 4B cells (200 ng) was bisulphite converted using EZ DNA Methylation‐Gold kit (Zymo Research). .. Primers for amplification of bisulphite converted DNA were designed using methprimer .

    Bisulfite Sequencing:

    Article Title: Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppression
    Article Snippet: Reduced Representation Bisulfite sequencing (RRBS-seq) For RRBS-seq analysis, Chr4-cl WT and KO ES cells were grown in either standard ES cell media containing FCS or for one week in 2i media containing vitamin C as described previously ( ). .. Genomic DNA was purified from WT and Chr4-cl KO ES cells using the Quick-gDNA purification kit (Zymo Research) and bisulfite-converted with the NEXTflex™ Bisulfite-Seq Kit (Bio Scientific) using Msp1 digestion to fragment DNA. ..

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  • 97
    Zymo Research genomic dna
    Confirmation of novel ETn insertions identified by capture-seq. (A) PCR confirmation of novel ETn insertions in genomic <t>DNA</t> of three littermates (IDs: T09673, T09674 and T00436) and their parents (T3913 and T3921). Primer sequences are shown in Table S5. (B) Heatmap shows Capture-Seq read counts (RPM) of a <t>Chr4-cl</t> KO mouse (ID: C6733) as determined in different tissues. Each row represents a novel ETn loci that was identified in at least one tissue. The color gradient indicates log10(RPM+1). (C) Heatmap shows the Capture-Seq RPM in technical replicates using the same Chr4-cl KO DNA sample (rep1/rep2) or replicates with DNA samples prepared from different sections of the tail from the same mouse at different ages (tail1/tail2). Each row represents a novel ETn loci that was identified in at least one of the displayed samples. The color gradient indicates log10(RPM+1). (D) ETn Capture-Seq read counts (RPM) at putative novel somatic (loci identified exclusively in one single animal) and germ-line (loci identified in several littermates) insertions.
    Genomic Dna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genomic dna/product/Zymo Research
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    genomic dna - by Bioz Stars, 2021-03
    97/100 stars
      Buy from Supplier

    98
    Zymo Research genomic dna clean concentrator 10 kit
    CTAB extraction test. Effect of extraction method on PCR success (%) measured as the number of positive amplicons divided by the total number of samples, before and after using Genomic <t>DNA</t> Clean Concentrator-10 kit. (A) ITS5 bryo- ITSC bryo, (B) ITS5D bryo- ITS4 bryo, (C) trnT-trnF , (D) rps4 , (E) ITS5 bryo- ITSC bryo, ITS5D bryo- ITS4 bryo, trnT-trnF , rps4 .
    Genomic Dna Clean Concentrator 10 Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genomic dna clean concentrator 10 kit/product/Zymo Research
    Average 98 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    genomic dna clean concentrator 10 kit - by Bioz Stars, 2021-03
    98/100 stars
      Buy from Supplier

    Image Search Results


    Confirmation of novel ETn insertions identified by capture-seq. (A) PCR confirmation of novel ETn insertions in genomic DNA of three littermates (IDs: T09673, T09674 and T00436) and their parents (T3913 and T3921). Primer sequences are shown in Table S5. (B) Heatmap shows Capture-Seq read counts (RPM) of a Chr4-cl KO mouse (ID: C6733) as determined in different tissues. Each row represents a novel ETn loci that was identified in at least one tissue. The color gradient indicates log10(RPM+1). (C) Heatmap shows the Capture-Seq RPM in technical replicates using the same Chr4-cl KO DNA sample (rep1/rep2) or replicates with DNA samples prepared from different sections of the tail from the same mouse at different ages (tail1/tail2). Each row represents a novel ETn loci that was identified in at least one of the displayed samples. The color gradient indicates log10(RPM+1). (D) ETn Capture-Seq read counts (RPM) at putative novel somatic (loci identified exclusively in one single animal) and germ-line (loci identified in several littermates) insertions.

    Journal: bioRxiv

    Article Title: Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppression

    doi: 10.1101/2020.01.17.910679

    Figure Lengend Snippet: Confirmation of novel ETn insertions identified by capture-seq. (A) PCR confirmation of novel ETn insertions in genomic DNA of three littermates (IDs: T09673, T09674 and T00436) and their parents (T3913 and T3921). Primer sequences are shown in Table S5. (B) Heatmap shows Capture-Seq read counts (RPM) of a Chr4-cl KO mouse (ID: C6733) as determined in different tissues. Each row represents a novel ETn loci that was identified in at least one tissue. The color gradient indicates log10(RPM+1). (C) Heatmap shows the Capture-Seq RPM in technical replicates using the same Chr4-cl KO DNA sample (rep1/rep2) or replicates with DNA samples prepared from different sections of the tail from the same mouse at different ages (tail1/tail2). Each row represents a novel ETn loci that was identified in at least one of the displayed samples. The color gradient indicates log10(RPM+1). (D) ETn Capture-Seq read counts (RPM) at putative novel somatic (loci identified exclusively in one single animal) and germ-line (loci identified in several littermates) insertions.

    Article Snippet: Genomic DNA was purified from WT and Chr4-cl KO ES cells using the Quick-gDNA purification kit (Zymo Research) and bisulfite-converted with the NEXTflex™ Bisulfite-Seq Kit (Bio Scientific) using Msp1 digestion to fragment DNA.

    Techniques: Polymerase Chain Reaction

    ETn retrotransposition in Chr4-cl KO mice. (A) Pedigree of mice used for transposon insertion screening by capture-seq in mice of different strain backgrounds. The number of novel ETn insertions (only present in one animal) are indicated. For animals whose direct ancestors have not been screened, the ETn insertions are shown in parentheses since parental inheritance cannot be excluded in that case. Germ-line insertions are indicated by asterisks. All DNA samples were prepared from tail tissues unless noted (-S: spleen, -E: ear, -B:Blood) (B) Statistical analysis of ETn insertion frequency in tail tissue from 30 Chr4-cl KO, KO/WT and WT mice that derived from two different Chr4-cl KO/WT x KO/WT matings. Only DNA samples that were collected from juvenile tails were considered for this analysis. P-value was calculated using one-sided Wilcoxon Rank Sum Test. WT and KO/WT mice were combined for the statistical analysis.

    Journal: bioRxiv

    Article Title: Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppression

    doi: 10.1101/2020.01.17.910679

    Figure Lengend Snippet: ETn retrotransposition in Chr4-cl KO mice. (A) Pedigree of mice used for transposon insertion screening by capture-seq in mice of different strain backgrounds. The number of novel ETn insertions (only present in one animal) are indicated. For animals whose direct ancestors have not been screened, the ETn insertions are shown in parentheses since parental inheritance cannot be excluded in that case. Germ-line insertions are indicated by asterisks. All DNA samples were prepared from tail tissues unless noted (-S: spleen, -E: ear, -B:Blood) (B) Statistical analysis of ETn insertion frequency in tail tissue from 30 Chr4-cl KO, KO/WT and WT mice that derived from two different Chr4-cl KO/WT x KO/WT matings. Only DNA samples that were collected from juvenile tails were considered for this analysis. P-value was calculated using one-sided Wilcoxon Rank Sum Test. WT and KO/WT mice were combined for the statistical analysis.

    Article Snippet: Genomic DNA was purified from WT and Chr4-cl KO ES cells using the Quick-gDNA purification kit (Zymo Research) and bisulfite-converted with the NEXTflex™ Bisulfite-Seq Kit (Bio Scientific) using Msp1 digestion to fragment DNA.

    Techniques: Mouse Assay, Derivative Assay

    CTAB extraction test. Effect of extraction method on PCR success (%) measured as the number of positive amplicons divided by the total number of samples, before and after using Genomic DNA Clean Concentrator-10 kit. (A) ITS5 bryo- ITSC bryo, (B) ITS5D bryo- ITS4 bryo, (C) trnT-trnF , (D) rps4 , (E) ITS5 bryo- ITSC bryo, ITS5D bryo- ITS4 bryo, trnT-trnF , rps4 .

    Journal: PeerJ

    Article Title: At the crossroads of botanical collections and molecular genetics laboratory: a preliminary study of obtaining amplifiable DNA from moss herbarium material

    doi: 10.7717/peerj.9109

    Figure Lengend Snippet: CTAB extraction test. Effect of extraction method on PCR success (%) measured as the number of positive amplicons divided by the total number of samples, before and after using Genomic DNA Clean Concentrator-10 kit. (A) ITS5 bryo- ITSC bryo, (B) ITS5D bryo- ITS4 bryo, (C) trnT-trnF , (D) rps4 , (E) ITS5 bryo- ITSC bryo, ITS5D bryo- ITS4 bryo, trnT-trnF , rps4 .

    Article Snippet: In CTAB extraction tests, the Genomic DNA Clean & Concentrator-10 kit was additionally applied to all prepared DNA extracts.

    Techniques: Polymerase Chain Reaction

    Deletion of the gene encoding putative restriction enzyme ChyI. A) Scheme for targeted gene deletion. The pJGW03 chyI knockout vector is transformed into JWCH006 ( ΔpyrF ), and uracil prototrophy selects for integration at one of the 500-bp flanking regions, denoted by the gray boxes. 5′ integration is shown. The uracil prototroph is then plated on 5-FOA to select for loop-out of the pyrF cassette via homologous recombination between flanking region sequences. The two possible results are a return to the wild-type sequence or a clean chyI deletion. (B) Chromosomal map of the locus containing the ORF for chyI . The deleted region is indicated by the line below the diagram. Bent arrows depict primers used to verify deletion of chyI in the JWCH008 strain. (C) Gel depicting PCR products of the chyI region in the JWCH006 ∆ pyrF strain (2.3 kb) compared to the JWCH008 ∆ pyrF ∆ chyI strain (1.25 kb) amplified by the indicated primers (JG025 and JG028). 1: C. hydrothermalis JWCH006 genomic DNA; 2: C. hydrothermalis JWCH008 genomic DNA; 3: negative control; M: 1 kb DNA ladder (NEB).

    Journal: Biotechnology for Biofuels

    Article Title: Heterologous complementation of a pyrF deletion in Caldicellulosiruptor hydrothermalis generates a new host for the analysis of biomass deconstruction

    doi: 10.1186/s13068-014-0132-8

    Figure Lengend Snippet: Deletion of the gene encoding putative restriction enzyme ChyI. A) Scheme for targeted gene deletion. The pJGW03 chyI knockout vector is transformed into JWCH006 ( ΔpyrF ), and uracil prototrophy selects for integration at one of the 500-bp flanking regions, denoted by the gray boxes. 5′ integration is shown. The uracil prototroph is then plated on 5-FOA to select for loop-out of the pyrF cassette via homologous recombination between flanking region sequences. The two possible results are a return to the wild-type sequence or a clean chyI deletion. (B) Chromosomal map of the locus containing the ORF for chyI . The deleted region is indicated by the line below the diagram. Bent arrows depict primers used to verify deletion of chyI in the JWCH008 strain. (C) Gel depicting PCR products of the chyI region in the JWCH006 ∆ pyrF strain (2.3 kb) compared to the JWCH008 ∆ pyrF ∆ chyI strain (1.25 kb) amplified by the indicated primers (JG025 and JG028). 1: C. hydrothermalis JWCH006 genomic DNA; 2: C. hydrothermalis JWCH008 genomic DNA; 3: negative control; M: 1 kb DNA ladder (NEB).

    Article Snippet: When the media was turbid, chromosomal DNA was extracted with a Zymo Research gDNA Extraction kit (Irvine, CA).

    Techniques: Knock-Out, Plasmid Preparation, Transformation Assay, Homologous Recombination, Sequencing, Polymerase Chain Reaction, Amplification, Negative Control

    Isolation of a spontaneous pyrF mutant in C. hydrothermalis . (A) Chromosomal map of the uridine monophosphate (UMP) biosynthetic gene cluster in C. hydrothermalis JWCH006. The 99-bp spontaneous deletion in ∆pyrF is indicated by the line below the diagram. 462 bp lie upstream and 357 bp lie downstream of the deletion. Bent arrows depict primers used to verify the structure of the pyrF gene in the JWCH006 strain. (B) Gel depicting PCR products of the pyrF region in the wild-type strain (1.13 kb) compared to the JWCH006 strain (1.02 kb) amplified by the indicated primers (DC163 and DC164). M: 1 kb DNA ladder (NEB); 1: wild-type genomic DNA; 2: JWCH006 genomic DNA; 3: negative control.

    Journal: Biotechnology for Biofuels

    Article Title: Heterologous complementation of a pyrF deletion in Caldicellulosiruptor hydrothermalis generates a new host for the analysis of biomass deconstruction

    doi: 10.1186/s13068-014-0132-8

    Figure Lengend Snippet: Isolation of a spontaneous pyrF mutant in C. hydrothermalis . (A) Chromosomal map of the uridine monophosphate (UMP) biosynthetic gene cluster in C. hydrothermalis JWCH006. The 99-bp spontaneous deletion in ∆pyrF is indicated by the line below the diagram. 462 bp lie upstream and 357 bp lie downstream of the deletion. Bent arrows depict primers used to verify the structure of the pyrF gene in the JWCH006 strain. (B) Gel depicting PCR products of the pyrF region in the wild-type strain (1.13 kb) compared to the JWCH006 strain (1.02 kb) amplified by the indicated primers (DC163 and DC164). M: 1 kb DNA ladder (NEB); 1: wild-type genomic DNA; 2: JWCH006 genomic DNA; 3: negative control.

    Article Snippet: When the media was turbid, chromosomal DNA was extracted with a Zymo Research gDNA Extraction kit (Irvine, CA).

    Techniques: Isolation, Mutagenesis, Polymerase Chain Reaction, Amplification, Negative Control