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NimbleGen Systems GmbH tiling genomic dna microarrays
mV H –CTCF consensus motif is a major determinant of CTCF binding at the murine IgH locus. ChIP with an α-CTCF antibody was performed on CD19 + pro-B cells that were isolated from 8- to 9-week-old RAG2 −/− mice and expanded for 3 days in the presence of IL-7 (10 ng/ml). Cy3-labeled input <t>DNA</t> and Cy5-labeled immunoprecipitated DNA were hybridized to customized tiling DNA <t>microarrays,</t> and peaks were called by the Ringo method . a , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites in the V H domain of the murine IgH locus ( cyan ) and observed CTCF peaks ( yellow ). b , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites ( cyan ); CTCF peaks were observed by ChIP-chip ( yellow ), and CTCF peaks were observed previously by ChIP-seq . c , enoLOGOS representation of three distinct sequence motifs identified by MEME analysis of the 79 CTCF peaks observed by ChIP-chip that did not contain an mV H –CTCF consensus motif.
Tiling Genomic Dna Microarrays, supplied by NimbleGen Systems GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF"

Article Title: The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.RA118.007348

mV H –CTCF consensus motif is a major determinant of CTCF binding at the murine IgH locus. ChIP with an α-CTCF antibody was performed on CD19 + pro-B cells that were isolated from 8- to 9-week-old RAG2 −/− mice and expanded for 3 days in the presence of IL-7 (10 ng/ml). Cy3-labeled input DNA and Cy5-labeled immunoprecipitated DNA were hybridized to customized tiling DNA microarrays, and peaks were called by the Ringo method . a , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites in the V H domain of the murine IgH locus ( cyan ) and observed CTCF peaks ( yellow ). b , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites ( cyan ); CTCF peaks were observed by ChIP-chip ( yellow ), and CTCF peaks were observed previously by ChIP-seq . c , enoLOGOS representation of three distinct sequence motifs identified by MEME analysis of the 79 CTCF peaks observed by ChIP-chip that did not contain an mV H –CTCF consensus motif.
Figure Legend Snippet: mV H –CTCF consensus motif is a major determinant of CTCF binding at the murine IgH locus. ChIP with an α-CTCF antibody was performed on CD19 + pro-B cells that were isolated from 8- to 9-week-old RAG2 −/− mice and expanded for 3 days in the presence of IL-7 (10 ng/ml). Cy3-labeled input DNA and Cy5-labeled immunoprecipitated DNA were hybridized to customized tiling DNA microarrays, and peaks were called by the Ringo method . a , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites in the V H domain of the murine IgH locus ( cyan ) and observed CTCF peaks ( yellow ). b , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites ( cyan ); CTCF peaks were observed by ChIP-chip ( yellow ), and CTCF peaks were observed previously by ChIP-seq . c , enoLOGOS representation of three distinct sequence motifs identified by MEME analysis of the 79 CTCF peaks observed by ChIP-chip that did not contain an mV H –CTCF consensus motif.

Techniques Used: Binding Assay, Isolation, Labeling, Immunoprecipitation, ChIP-chip, ChIP-sequencing, Sequencing

Related Articles

Sequencing:

Article Title: The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF
Article Snippet: .. Tiling genomic DNA microarrays were custom-designed (NimbleGen Systems, Inc.) based on the mm9 release of the IgH locus sequence (murine chr12: 114,341,024–117,349,200). ..

Article Title: The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF
Article Snippet: .. Tiling genomic DNA microarrays were custom designed (NimbleGen Systems, Inc) based on the mm9 release of the IgH locus sequence (murine chr12: 114,341,024–117,349,200). ..

Article Title: Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination
Article Snippet: .. Tiling genomic DNA microarrays were custom designed (NimbleGen Systems) based on the University of California, Santa Cruz mm9 release of sequence of the IgH locus: murine chr12: 114,341,024 to 117,349,200. ..

Immunoprecipitation:

Article Title: Core 2 ß1,6-N-acetylglucosaminyltransferase-I, crucial for P-selectin ligand expression is controlled by a distal enhancer regulated by STAT4 and T-bet in CD4+ T helper cells 1.
Article Snippet: P-selectin ligands (P-ligs) support the recruitment of lymphocytes into inflamed tissues.. Binding to Pselectin is mediated by oligosaccharide groups synthesized by means of several glycosyltransferases including core 2 ß1,6-N-acetylglucosaminyltransferase-I (C2GlcNAcT-I), encoded by the gene Gcnt1.. Using Gcnt1−/− Th1 cells, we show that C2GlcNAcT-I is crucial for inflammatory T cell homing in vivo.

Amplification:

Article Title: Core 2 ß1,6-N-acetylglucosaminyltransferase-I, crucial for P-selectin ligand expression is controlled by a distal enhancer regulated by STAT4 and T-bet in CD4+ T helper cells 1.
Article Snippet: P-selectin ligands (P-ligs) support the recruitment of lymphocytes into inflamed tissues.. Binding to Pselectin is mediated by oligosaccharide groups synthesized by means of several glycosyltransferases including core 2 ß1,6-N-acetylglucosaminyltransferase-I (C2GlcNAcT-I), encoded by the gene Gcnt1.. Using Gcnt1−/− Th1 cells, we show that C2GlcNAcT-I is crucial for inflammatory T cell homing in vivo.

Whole Genome Amplification:

Article Title: Core 2 ß1,6-N-acetylglucosaminyltransferase-I, crucial for P-selectin ligand expression is controlled by a distal enhancer regulated by STAT4 and T-bet in CD4+ T helper cells 1.
Article Snippet: P-selectin ligands (P-ligs) support the recruitment of lymphocytes into inflamed tissues.. Binding to Pselectin is mediated by oligosaccharide groups synthesized by means of several glycosyltransferases including core 2 ß1,6-N-acetylglucosaminyltransferase-I (C2GlcNAcT-I), encoded by the gene Gcnt1.. Using Gcnt1−/− Th1 cells, we show that C2GlcNAcT-I is crucial for inflammatory T cell homing in vivo.

Microarray:

Article Title: Core 2 ß1,6-N-acetylglucosaminyltransferase-I, crucial for P-selectin ligand expression is controlled by a distal enhancer regulated by STAT4 and T-bet in CD4+ T helper cells 1.
Article Snippet: P-selectin ligands (P-ligs) support the recruitment of lymphocytes into inflamed tissues.. Binding to Pselectin is mediated by oligosaccharide groups synthesized by means of several glycosyltransferases including core 2 ß1,6-N-acetylglucosaminyltransferase-I (C2GlcNAcT-I), encoded by the gene Gcnt1.. Using Gcnt1−/− Th1 cells, we show that C2GlcNAcT-I is crucial for inflammatory T cell homing in vivo.

Labeling:

Article Title: Senescence is an Endogenous Trigger for microRNA-Directed Transcriptional Gene Silencing in Human Cells
Article Snippet: .. The labeling and hybridisation of DNA from input and IP fractions for ChIP-chip analysis were performed by NimbleGen Systems, Inc. Fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). ..

Article Title: Functional Conservation of the Glide/Gcm Regulatory Network Controlling Glia, Hemocyte, and Tendon Cell Differentiation in Drosophila
Article Snippet: .. The Dam-only and Dam-Gcm samples were labeled and hybridized together on a whole-genome 2.1 million–feature tiling array with 50- to 75-mer oligonucleotides spaced at ∼55-bp intervals (Nimblegen Systems). .. Arrays were scanned and intensities extracted (Nimblegen Systems).

Hybridization:

Article Title: Senescence is an Endogenous Trigger for microRNA-Directed Transcriptional Gene Silencing in Human Cells
Article Snippet: .. The labeling and hybridisation of DNA from input and IP fractions for ChIP-chip analysis were performed by NimbleGen Systems, Inc. Fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). ..

ChIP-chip:

Article Title: Senescence is an Endogenous Trigger for microRNA-Directed Transcriptional Gene Silencing in Human Cells
Article Snippet: .. The labeling and hybridisation of DNA from input and IP fractions for ChIP-chip analysis were performed by NimbleGen Systems, Inc. Fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). ..

Fluorescence:

Article Title: Senescence is an Endogenous Trigger for microRNA-Directed Transcriptional Gene Silencing in Human Cells
Article Snippet: .. The labeling and hybridisation of DNA from input and IP fractions for ChIP-chip analysis were performed by NimbleGen Systems, Inc. Fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). ..

Extraction:

Article Title: Senescence is an Endogenous Trigger for microRNA-Directed Transcriptional Gene Silencing in Human Cells
Article Snippet: .. The labeling and hybridisation of DNA from input and IP fractions for ChIP-chip analysis were performed by NimbleGen Systems, Inc. Fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). ..

Software:

Article Title: Senescence is an Endogenous Trigger for microRNA-Directed Transcriptional Gene Silencing in Human Cells
Article Snippet: .. The labeling and hybridisation of DNA from input and IP fractions for ChIP-chip analysis were performed by NimbleGen Systems, Inc. Fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). ..

other:

Article Title: The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF
Article Snippet: For primer and probe sequences see Supplementary Table 4. by gest on July 0, 2019 hp://w w w .jb.org/ D ow nladed from CTCF binds evolutionarily conserved sites in the IgH locus 11 Microarray hybridization and processing Tiling genomic DNA microarrays were custom designed (NimbleGen Systems, Inc) based on the mm9 release of the IgH locus sequence (murine chr12: 114,341,024–117,349,200).

Tiling:

Article Title: Functional Conservation of the Glide/Gcm Regulatory Network Controlling Glia, Hemocyte, and Tendon Cell Differentiation in Drosophila
Article Snippet: .. The Dam-only and Dam-Gcm samples were labeled and hybridized together on a whole-genome 2.1 million–feature tiling array with 50- to 75-mer oligonucleotides spaced at ∼55-bp intervals (Nimblegen Systems). .. Arrays were scanned and intensities extracted (Nimblegen Systems).



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mV H –CTCF consensus motif is a major determinant of CTCF binding at the murine IgH locus. ChIP with an α-CTCF antibody was performed on CD19 + pro-B cells that were isolated from 8- to 9-week-old RAG2 −/− mice and expanded for 3 days in the presence of IL-7 (10 ng/ml). Cy3-labeled input <t>DNA</t> and Cy5-labeled immunoprecipitated DNA were hybridized to customized tiling DNA <t>microarrays,</t> and peaks were called by the Ringo method . a , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites in the V H domain of the murine IgH locus ( cyan ) and observed CTCF peaks ( yellow ). b , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites ( cyan ); CTCF peaks were observed by ChIP-chip ( yellow ), and CTCF peaks were observed previously by ChIP-seq . c , enoLOGOS representation of three distinct sequence motifs identified by MEME analysis of the 79 CTCF peaks observed by ChIP-chip that did not contain an mV H –CTCF consensus motif.
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mV H –CTCF consensus motif is a major determinant of CTCF binding at the murine IgH locus. ChIP with an α-CTCF antibody was performed on CD19 + pro-B cells that were isolated from 8- to 9-week-old RAG2 −/− mice and expanded for 3 days in the presence of IL-7 (10 ng/ml). Cy3-labeled input <t>DNA</t> and Cy5-labeled immunoprecipitated DNA were hybridized to customized tiling DNA <t>microarrays,</t> and peaks were called by the Ringo method . a , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites in the V H domain of the murine IgH locus ( cyan ) and observed CTCF peaks ( yellow ). b , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites ( cyan ); CTCF peaks were observed by ChIP-chip ( yellow ), and CTCF peaks were observed previously by ChIP-seq . c , enoLOGOS representation of three distinct sequence motifs identified by MEME analysis of the 79 CTCF peaks observed by ChIP-chip that did not contain an mV H –CTCF consensus motif.
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Image Search Results


mV H –CTCF consensus motif is a major determinant of CTCF binding at the murine IgH locus. ChIP with an α-CTCF antibody was performed on CD19 + pro-B cells that were isolated from 8- to 9-week-old RAG2 −/− mice and expanded for 3 days in the presence of IL-7 (10 ng/ml). Cy3-labeled input DNA and Cy5-labeled immunoprecipitated DNA were hybridized to customized tiling DNA microarrays, and peaks were called by the Ringo method . a , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites in the V H domain of the murine IgH locus ( cyan ) and observed CTCF peaks ( yellow ). b , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites ( cyan ); CTCF peaks were observed by ChIP-chip ( yellow ), and CTCF peaks were observed previously by ChIP-seq . c , enoLOGOS representation of three distinct sequence motifs identified by MEME analysis of the 79 CTCF peaks observed by ChIP-chip that did not contain an mV H –CTCF consensus motif.

Journal: The Journal of Biological Chemistry

Article Title: The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF

doi: 10.1074/jbc.RA118.007348

Figure Lengend Snippet: mV H –CTCF consensus motif is a major determinant of CTCF binding at the murine IgH locus. ChIP with an α-CTCF antibody was performed on CD19 + pro-B cells that were isolated from 8- to 9-week-old RAG2 −/− mice and expanded for 3 days in the presence of IL-7 (10 ng/ml). Cy3-labeled input DNA and Cy5-labeled immunoprecipitated DNA were hybridized to customized tiling DNA microarrays, and peaks were called by the Ringo method . a , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites in the V H domain of the murine IgH locus ( cyan ) and observed CTCF peaks ( yellow ). b , area-proportional Venn diagram showing the overlap between predicted CTCF-binding sites ( cyan ); CTCF peaks were observed by ChIP-chip ( yellow ), and CTCF peaks were observed previously by ChIP-seq . c , enoLOGOS representation of three distinct sequence motifs identified by MEME analysis of the 79 CTCF peaks observed by ChIP-chip that did not contain an mV H –CTCF consensus motif.

Article Snippet: Tiling genomic DNA microarrays were custom-designed (NimbleGen Systems, Inc.) based on the mm9 release of the IgH locus sequence (murine chr12: 114,341,024–117,349,200).

Techniques: Binding Assay, Isolation, Labeling, Immunoprecipitation, ChIP-chip, ChIP-sequencing, Sequencing