chromatin immunoprecipitation chromatin  (Covaris)


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    Name:
    truChIP Chromatin Shearing Kit with Formaldehyde
    Description:
    The truChIP Chromatin Shearing Kit with Formaldehyde is designed and optimized for the efficient and reproducible shearing of chromatin from cultured mammalian cells suspension or adherent using the Covaris Adaptive Focused Acoustics AFA technology
    Catalog Number:
    520154
    Price:
    None
    Applications:
    Chromatin shearing
    Category:
    Reagent
    Quantity:
    1 0
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    Structured Review

    Covaris chromatin immunoprecipitation chromatin
    truChIP Chromatin Shearing Kit with Formaldehyde
    The truChIP Chromatin Shearing Kit with Formaldehyde is designed and optimized for the efficient and reproducible shearing of chromatin from cultured mammalian cells suspension or adherent using the Covaris Adaptive Focused Acoustics AFA technology
    https://www.bioz.com/result/chromatin immunoprecipitation chromatin/product/Covaris
    Average 94 stars, based on 421 article reviews
    Price from $9.99 to $1999.99
    chromatin immunoprecipitation chromatin - by Bioz Stars, 2020-08
    94/100 stars

    Images

    1) Product Images from "EMT is associated with an epigenetic signature of ECM remodeling genes"

    Article Title: EMT is associated with an epigenetic signature of ECM remodeling genes

    Journal: Cell Death & Disease

    doi: 10.1038/s41419-019-1397-4

    Epigenetic regulation in epidermal growth factor (EGF)-induced epithelial–mesenchymal transition (EMT) in MDA-MB-468 cells. a Representative images showing a change in morphology of MDA-MB-468 cells following 1–5 days of treatment with EGF (20 or 50 ng/ml). b Validation of EMT markers by quantitative reverse transcriptase–polymerase chain reaction (qRT-PCR) in the MDA-MB-468 cell line treated or not with EGF (20 or 50 ng/ml) for 3 days (mean ± SD of at least 3 independent experiments). c Increased change of morphology and intensity of VIMENTIN staining using immunofluorescence (IF) in MDA-MB-468 cells treated or not with EGF (20 or 50 ng/ml) for 3 days. d Increased expression of SNAIL1 in MDA-MB-468 cells treated or not with EGF (20 or 50 ng/ml) for 3 days. e Increased staining in H3K4me2 and H3K27me3 marks using IF in MDA-MB-468 cells treated or not with EGF (20 or 50 ng/ml) for 3 days (representative pictures of 3 independent experiments). f Increased expression of ADAM19 gene quantified by qRT-PCR in MDA-MB-468 cells treated or not with EGF (50 ng/ml) for 3 days. g Ratio of fold change (EMT: EGF treated versus NT: untreated MDA-MB-468 cells) following chromatin immunoprecipitation against H3K4me2 and H3K27me3 marks on the ADAM19 promoter. Dotted line = 1 (mean ± SEM of at least 3 independent experiments) * p
    Figure Legend Snippet: Epigenetic regulation in epidermal growth factor (EGF)-induced epithelial–mesenchymal transition (EMT) in MDA-MB-468 cells. a Representative images showing a change in morphology of MDA-MB-468 cells following 1–5 days of treatment with EGF (20 or 50 ng/ml). b Validation of EMT markers by quantitative reverse transcriptase–polymerase chain reaction (qRT-PCR) in the MDA-MB-468 cell line treated or not with EGF (20 or 50 ng/ml) for 3 days (mean ± SD of at least 3 independent experiments). c Increased change of morphology and intensity of VIMENTIN staining using immunofluorescence (IF) in MDA-MB-468 cells treated or not with EGF (20 or 50 ng/ml) for 3 days. d Increased expression of SNAIL1 in MDA-MB-468 cells treated or not with EGF (20 or 50 ng/ml) for 3 days. e Increased staining in H3K4me2 and H3K27me3 marks using IF in MDA-MB-468 cells treated or not with EGF (20 or 50 ng/ml) for 3 days (representative pictures of 3 independent experiments). f Increased expression of ADAM19 gene quantified by qRT-PCR in MDA-MB-468 cells treated or not with EGF (50 ng/ml) for 3 days. g Ratio of fold change (EMT: EGF treated versus NT: untreated MDA-MB-468 cells) following chromatin immunoprecipitation against H3K4me2 and H3K27me3 marks on the ADAM19 promoter. Dotted line = 1 (mean ± SEM of at least 3 independent experiments) * p

    Techniques Used: Multiple Displacement Amplification, Polymerase Chain Reaction, Quantitative RT-PCR, Staining, Immunofluorescence, Expressing, Chromatin Immunoprecipitation

    Chromatin immunoprecipitation (ChIP) and ChIP-seq analysis on the H3K4me2 mark following transforming growth factor beta (TGFβ)/tumor necrosis factor alpha (TGFβ/TNFα) treatment. a Volcano plot of the 42,076 H3K4me2 merged islands. In red, the regions significantly enriched in TGFβ-/TNFα-treated cells versus non-treated cells. FC: fold change treated versus non-treated. fdr: false discovery rate treated versus non-treated. b Activating and/or repressive function prediction of H3K4me2 in A549 cells. BETA-basic integrates H3K4me2 differentially enriched regions and transcriptome data on TGFβ/TNFα treated cells and non-treated conditions to identify upregulated (red) and downregulated (purple) genes. The dashed line indicates the non-differentially expressed genes as background. Genes are cumulated by the rank on the basis of the regulatory potential score from high to low. p Values represent the significance of difference in the upregulated or downregulated groups compared with the non-differentially expressed group by Kolmogorov–Smirnov test. c Integration of transcriptome and ChIP-seq data for the A549 cell line. Top: heat maps of read coverage from −5 kb to +5 kb around the transcription start site for TGFβ-/TNFα-treated (left) and non-treated (right) conditions. Each line represents an upregulated gene identified by BETA. Genes are ordered according to their increasing rank product. Upper panels: read coverage density plots. Bottom: Corresponding gene expression heat map for treated ( n = 4) and non-treated conditions ( n = 4). Black lines indicate differentially expressed genes. d Increase expression of ADAM19 and MMP9 and decrease expression of SCNN1A in A549 cells treated with TGFβ/TNFα (mean ± SD of at least 3 independent experiments). e Ratio of fold change (epithelial–mesenchymal transition: TGFβ/TNFα treated A549 versus NT: untreated A549 cells) following ChIP against H3K4me2 and H3K27me3 marks on MMP9 , ADAM19 , and SCNN1A promoters. Dotted line = 1 (mean ± SEM of at least 3 independent experiments) * p
    Figure Legend Snippet: Chromatin immunoprecipitation (ChIP) and ChIP-seq analysis on the H3K4me2 mark following transforming growth factor beta (TGFβ)/tumor necrosis factor alpha (TGFβ/TNFα) treatment. a Volcano plot of the 42,076 H3K4me2 merged islands. In red, the regions significantly enriched in TGFβ-/TNFα-treated cells versus non-treated cells. FC: fold change treated versus non-treated. fdr: false discovery rate treated versus non-treated. b Activating and/or repressive function prediction of H3K4me2 in A549 cells. BETA-basic integrates H3K4me2 differentially enriched regions and transcriptome data on TGFβ/TNFα treated cells and non-treated conditions to identify upregulated (red) and downregulated (purple) genes. The dashed line indicates the non-differentially expressed genes as background. Genes are cumulated by the rank on the basis of the regulatory potential score from high to low. p Values represent the significance of difference in the upregulated or downregulated groups compared with the non-differentially expressed group by Kolmogorov–Smirnov test. c Integration of transcriptome and ChIP-seq data for the A549 cell line. Top: heat maps of read coverage from −5 kb to +5 kb around the transcription start site for TGFβ-/TNFα-treated (left) and non-treated (right) conditions. Each line represents an upregulated gene identified by BETA. Genes are ordered according to their increasing rank product. Upper panels: read coverage density plots. Bottom: Corresponding gene expression heat map for treated ( n = 4) and non-treated conditions ( n = 4). Black lines indicate differentially expressed genes. d Increase expression of ADAM19 and MMP9 and decrease expression of SCNN1A in A549 cells treated with TGFβ/TNFα (mean ± SD of at least 3 independent experiments). e Ratio of fold change (epithelial–mesenchymal transition: TGFβ/TNFα treated A549 versus NT: untreated A549 cells) following ChIP against H3K4me2 and H3K27me3 marks on MMP9 , ADAM19 , and SCNN1A promoters. Dotted line = 1 (mean ± SEM of at least 3 independent experiments) * p

    Techniques Used: Chromatin Immunoprecipitation, Expressing

    Related Articles

    Multiplex Assay:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

    RNA Sequencing Assay:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

    Sonication:

    Article Title: Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells
    Article Snippet: .. Chip-seq library preparation and sequencing Chromatin was prepared from pellets of 5 106 NESCs following the truChIP Chromatin Sheering Kit standard protocol (Covaris Inc.) and sonicated to obtain DNA fragments averaging 200 bp. .. 10 ng of DNA immunoprecipitated with anti-H3K4me1 and anti-H3K4me3 antibodies (Ab8895 and Ab8580, Abcam Plc.) or control input DNA were used to prepare the sequencing libraries, which were checked by capillary electrophoresis and sequenced in one lane of a single-strand 50 bp GAIIx Illumina Run ( and Methods).

    Isolation:

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). .. Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200–500bp.

    Article Title: PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance
    Article Snippet: .. Chromatin was prepared from isolated acinar cells or cell lines using the truChIP chromatin-shearing reagent kit (Covaris, 520154). .. Chromatin was sheared in 1-mL millitubes (Covaris, 520135) using a Covaris S200 (5% duty cycle, intensity of 4, 200 cycles per burst, for 8 min) to obtain chromatin fragments 100–700 base pairs in length.

    Polyacrylamide Gel Electrophoresis:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

    Protease Inhibitor:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

    Sequencing:

    Article Title: Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells
    Article Snippet: .. Chip-seq library preparation and sequencing Chromatin was prepared from pellets of 5 106 NESCs following the truChIP Chromatin Sheering Kit standard protocol (Covaris Inc.) and sonicated to obtain DNA fragments averaging 200 bp. .. 10 ng of DNA immunoprecipitated with anti-H3K4me1 and anti-H3K4me3 antibodies (Ab8895 and Ab8580, Abcam Plc.) or control input DNA were used to prepare the sequencing libraries, which were checked by capillary electrophoresis and sequenced in one lane of a single-strand 50 bp GAIIx Illumina Run ( and Methods).

    Staining:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

    Lysis:

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). .. Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200–500bp.

    Recombinant:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

    Chromatin Immunoprecipitation:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

    Article Title: EMT is associated with an epigenetic signature of ECM remodeling genes
    Article Snippet: .. Chromatin immunoprecipitation Chromatin was prepared using the truChIP™ Chromatin Shearing Kit (520154, Covaris, France) according to the manufacturer’s instructions. .. Each sample was submitted to a 8 min sonicated using the M220 Covaris sonicator.

    ChIP-sequencing:

    Article Title: Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells
    Article Snippet: .. Chip-seq library preparation and sequencing Chromatin was prepared from pellets of 5 106 NESCs following the truChIP Chromatin Sheering Kit standard protocol (Covaris Inc.) and sonicated to obtain DNA fragments averaging 200 bp. .. 10 ng of DNA immunoprecipitated with anti-H3K4me1 and anti-H3K4me3 antibodies (Ab8895 and Ab8580, Abcam Plc.) or control input DNA were used to prepare the sequencing libraries, which were checked by capillary electrophoresis and sequenced in one lane of a single-strand 50 bp GAIIx Illumina Run ( and Methods).

    DC Protein Assay:

    Article Title: Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination.
    Article Snippet: .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. .. An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism.

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