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Illumina Inc chip input dna
Genome-wide characterization of <t>Runx2</t> occupied regions (R2ORs). C4-2B/Rx2 dox cells were subjected to Runx2 ChIP-seq analysis after dox treatment and immunoprecipitation of Runx2-bound <t>DNA</t> fragments with anti-FLAG antibodies. ( A ) ChIP-seq results showing R2ORs upstream of the KLK and CSF2 TSS s . Raw ChIP-seq data are presented as frequency of reads per location for 30 kb of DNA sequences at the KLK2 (top) and CSF2 (bottom) loci. For each locus, the upper track shows results for chromatin aliquoted prior to immunoprecipitation (input). Regions investigated in Figure 1 by conventional ChIP assays are marked by black bars. ( B ) Sixteen Runx2 ChIP-seq peaks were validated by conventional ChIP-qPCR and the ChIP-seq scores are plotted against the qPCR enrichment factors. ( C ) Distance from the 1603 top R2ORs to the nearest TSS were mapped (red) and are shown along with control distribution patterns of 1000 sets of 1603 matched random sequences (gray). Y -axis values are numbers of R2ORs per 15 kb window. ( D ) Genomic distribution of the 1603 top R2ORs (red bars) versus that of 1000 sets of matched random sequences (gray bars; mean ± SD). TSS refers to −1000 to +100 bp from 5′-end of annotated RNA. Transcription Termination Site ( TTS ) is defined as −100 to +1000 bp from the 3′-end of the transcript. Inset shows blow up of TTS and TTS data.
Chip Input Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion"

Article Title: Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkr1219

Genome-wide characterization of Runx2 occupied regions (R2ORs). C4-2B/Rx2 dox cells were subjected to Runx2 ChIP-seq analysis after dox treatment and immunoprecipitation of Runx2-bound DNA fragments with anti-FLAG antibodies. ( A ) ChIP-seq results showing R2ORs upstream of the KLK and CSF2 TSS s . Raw ChIP-seq data are presented as frequency of reads per location for 30 kb of DNA sequences at the KLK2 (top) and CSF2 (bottom) loci. For each locus, the upper track shows results for chromatin aliquoted prior to immunoprecipitation (input). Regions investigated in Figure 1 by conventional ChIP assays are marked by black bars. ( B ) Sixteen Runx2 ChIP-seq peaks were validated by conventional ChIP-qPCR and the ChIP-seq scores are plotted against the qPCR enrichment factors. ( C ) Distance from the 1603 top R2ORs to the nearest TSS were mapped (red) and are shown along with control distribution patterns of 1000 sets of 1603 matched random sequences (gray). Y -axis values are numbers of R2ORs per 15 kb window. ( D ) Genomic distribution of the 1603 top R2ORs (red bars) versus that of 1000 sets of matched random sequences (gray bars; mean ± SD). TSS refers to −1000 to +100 bp from 5′-end of annotated RNA. Transcription Termination Site ( TTS ) is defined as −100 to +1000 bp from the 3′-end of the transcript. Inset shows blow up of TTS and TTS data.
Figure Legend Snippet: Genome-wide characterization of Runx2 occupied regions (R2ORs). C4-2B/Rx2 dox cells were subjected to Runx2 ChIP-seq analysis after dox treatment and immunoprecipitation of Runx2-bound DNA fragments with anti-FLAG antibodies. ( A ) ChIP-seq results showing R2ORs upstream of the KLK and CSF2 TSS s . Raw ChIP-seq data are presented as frequency of reads per location for 30 kb of DNA sequences at the KLK2 (top) and CSF2 (bottom) loci. For each locus, the upper track shows results for chromatin aliquoted prior to immunoprecipitation (input). Regions investigated in Figure 1 by conventional ChIP assays are marked by black bars. ( B ) Sixteen Runx2 ChIP-seq peaks were validated by conventional ChIP-qPCR and the ChIP-seq scores are plotted against the qPCR enrichment factors. ( C ) Distance from the 1603 top R2ORs to the nearest TSS were mapped (red) and are shown along with control distribution patterns of 1000 sets of 1603 matched random sequences (gray). Y -axis values are numbers of R2ORs per 15 kb window. ( D ) Genomic distribution of the 1603 top R2ORs (red bars) versus that of 1000 sets of matched random sequences (gray bars; mean ± SD). TSS refers to −1000 to +100 bp from 5′-end of annotated RNA. Transcription Termination Site ( TTS ) is defined as −100 to +1000 bp from the 3′-end of the transcript. Inset shows blow up of TTS and TTS data.

Techniques Used: Genome Wide, Chromatin Immunoprecipitation, Immunoprecipitation, Real-time Polymerase Chain Reaction

DNA sequence motifs enriched in R2ORs. Motifs enriched in R2ORs compared to 1603 matched random sequences were identified using HOMER 3.1. ( A ) Logo for the top motif ( Runx2 ) is shown above the Runx1 logo identified by Pencovich et al. ( 35 ). ( B ) Motifs identified after R2ORs were re-analyzed as in A following masking of the Runx2 motifs. ( C ) Motif statistics. P- values are for motif enrichment. The percentages of R2ORs containing at least one copy of each motif are indicated against the percentage of motif-containing random sequences. Motifs/R2OR indicates for each motif the average number of copies per R2OR in R2ORs containing at least one copy.
Figure Legend Snippet: DNA sequence motifs enriched in R2ORs. Motifs enriched in R2ORs compared to 1603 matched random sequences were identified using HOMER 3.1. ( A ) Logo for the top motif ( Runx2 ) is shown above the Runx1 logo identified by Pencovich et al. ( 35 ). ( B ) Motifs identified after R2ORs were re-analyzed as in A following masking of the Runx2 motifs. ( C ) Motif statistics. P- values are for motif enrichment. The percentages of R2ORs containing at least one copy of each motif are indicated against the percentage of motif-containing random sequences. Motifs/R2OR indicates for each motif the average number of copies per R2OR in R2ORs containing at least one copy.

Techniques Used: Sequencing

Related Articles

Amplification:

Article Title: CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Article Snippet: .. We used 100 ng of ChIP input DNA (as measured by Fragment analyzer) and 50 μl of immunoprecipitated DNA as a starting material; Illumina adapters were diluted 1:50, and library samples were enriched through 18 cycles of PCR amplification. .. We assessed library quality and fragment size by qPCR and Fragment analyzer, and when necessary we performed an additional size selection step on agarose gel after PCR amplification to enrich for fragments between 150 and 500 bp.

High Throughput Screening Assay:

Article Title: Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1
Article Snippet: .. ChIP DNA along with ChIP input DNA were prepared as described above, and high-throughput sequencing of the fragments was performed using the Illumina GAII platform. .. Enrichment for known target sequences was verified by SBYR green quantitative real-time PCR before ChIP and input DNA were sequenced.

Polymerase Chain Reaction:

Article Title: CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Article Snippet: .. We used 100 ng of ChIP input DNA (as measured by Fragment analyzer) and 50 μl of immunoprecipitated DNA as a starting material; Illumina adapters were diluted 1:50, and library samples were enriched through 18 cycles of PCR amplification. .. We assessed library quality and fragment size by qPCR and Fragment analyzer, and when necessary we performed an additional size selection step on agarose gel after PCR amplification to enrich for fragments between 150 and 500 bp.

Article Title: Methylated DNA is over-represented in whole-genome bisulfite sequencing data
Article Snippet: .. ChIP input DNA was used to prepare Illumina sequencing libraries using two different polymerases and PCR was performed for 4, 8, and 15 cycles. .. Libraries prepared using a TruSeq PCR master-mix revealed equal representation of GC-rich and AT-rich regions after 4 and 8 cycles of PCR, but a clear amplification bias was observed after 15 cycles of PCR ( Figures ).

Next-Generation Sequencing:

Article Title: Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion
Article Snippet: .. ChIP-sequencing and peak calling Runx2 ChIP DNA along with ChIP input DNA were prepared as above from C4-2B/Rx2dox cells treated with dox for 14 h, and high throughput sequencing of the 500–1000 bp fragments was performed using Illumina Hi-Seq 2000. ..

Immunoprecipitation:

Article Title: CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Article Snippet: .. We used 100 ng of ChIP input DNA (as measured by Fragment analyzer) and 50 μl of immunoprecipitated DNA as a starting material; Illumina adapters were diluted 1:50, and library samples were enriched through 18 cycles of PCR amplification. .. We assessed library quality and fragment size by qPCR and Fragment analyzer, and when necessary we performed an additional size selection step on agarose gel after PCR amplification to enrich for fragments between 150 and 500 bp.

Sequencing:

Article Title: Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1
Article Snippet: .. ChIP DNA along with ChIP input DNA were prepared as described above, and high-throughput sequencing of the fragments was performed using the Illumina GAII platform. .. Enrichment for known target sequences was verified by SBYR green quantitative real-time PCR before ChIP and input DNA were sequenced.

Article Title: Methylated DNA is over-represented in whole-genome bisulfite sequencing data
Article Snippet: .. ChIP input DNA was used to prepare Illumina sequencing libraries using two different polymerases and PCR was performed for 4, 8, and 15 cycles. .. Libraries prepared using a TruSeq PCR master-mix revealed equal representation of GC-rich and AT-rich regions after 4 and 8 cycles of PCR, but a clear amplification bias was observed after 15 cycles of PCR ( Figures ).

Article Title: Methylated DNA is over-represented in whole-genome bisulfite sequencing data
Article Snippet: .. For Illumina sequencing, libraries were prepared from 10 ng of ChIP input DNA using an Illumina TruSeq kit (Illumina cat-FC-121-2002). .. DNA adaptors were diluted 1:100 prior to ligation.

Chloramphenicol Acetyltransferase Assay:

Article Title: Methylated DNA is over-represented in whole-genome bisulfite sequencing data
Article Snippet: .. For Illumina sequencing, libraries were prepared from 10 ng of ChIP input DNA using an Illumina TruSeq kit (Illumina cat-FC-121-2002). .. DNA adaptors were diluted 1:100 prior to ligation.

Chromatin Immunoprecipitation:

Article Title: Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1
Article Snippet: .. ChIP DNA along with ChIP input DNA were prepared as described above, and high-throughput sequencing of the fragments was performed using the Illumina GAII platform. .. Enrichment for known target sequences was verified by SBYR green quantitative real-time PCR before ChIP and input DNA were sequenced.

Article Title: Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion
Article Snippet: .. ChIP-sequencing and peak calling Runx2 ChIP DNA along with ChIP input DNA were prepared as above from C4-2B/Rx2dox cells treated with dox for 14 h, and high throughput sequencing of the 500–1000 bp fragments was performed using Illumina Hi-Seq 2000. ..

Article Title: CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Article Snippet: .. We used 100 ng of ChIP input DNA (as measured by Fragment analyzer) and 50 μl of immunoprecipitated DNA as a starting material; Illumina adapters were diluted 1:50, and library samples were enriched through 18 cycles of PCR amplification. .. We assessed library quality and fragment size by qPCR and Fragment analyzer, and when necessary we performed an additional size selection step on agarose gel after PCR amplification to enrich for fragments between 150 and 500 bp.

Article Title: Methylated DNA is over-represented in whole-genome bisulfite sequencing data
Article Snippet: .. ChIP input DNA was used to prepare Illumina sequencing libraries using two different polymerases and PCR was performed for 4, 8, and 15 cycles. .. Libraries prepared using a TruSeq PCR master-mix revealed equal representation of GC-rich and AT-rich regions after 4 and 8 cycles of PCR, but a clear amplification bias was observed after 15 cycles of PCR ( Figures ).

Article Title: Methylated DNA is over-represented in whole-genome bisulfite sequencing data
Article Snippet: .. For Illumina sequencing, libraries were prepared from 10 ng of ChIP input DNA using an Illumina TruSeq kit (Illumina cat-FC-121-2002). .. DNA adaptors were diluted 1:100 prior to ligation.

ChIP-sequencing:

Article Title: Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion
Article Snippet: .. ChIP-sequencing and peak calling Runx2 ChIP DNA along with ChIP input DNA were prepared as above from C4-2B/Rx2dox cells treated with dox for 14 h, and high throughput sequencing of the 500–1000 bp fragments was performed using Illumina Hi-Seq 2000. ..

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    Illumina Inc chip input dna
    Genome-wide characterization of <t>Runx2</t> occupied regions (R2ORs). C4-2B/Rx2 dox cells were subjected to Runx2 ChIP-seq analysis after dox treatment and immunoprecipitation of Runx2-bound <t>DNA</t> fragments with anti-FLAG antibodies. ( A ) ChIP-seq results showing R2ORs upstream of the KLK and CSF2 TSS s . Raw ChIP-seq data are presented as frequency of reads per location for 30 kb of DNA sequences at the KLK2 (top) and CSF2 (bottom) loci. For each locus, the upper track shows results for chromatin aliquoted prior to immunoprecipitation (input). Regions investigated in Figure 1 by conventional ChIP assays are marked by black bars. ( B ) Sixteen Runx2 ChIP-seq peaks were validated by conventional ChIP-qPCR and the ChIP-seq scores are plotted against the qPCR enrichment factors. ( C ) Distance from the 1603 top R2ORs to the nearest TSS were mapped (red) and are shown along with control distribution patterns of 1000 sets of 1603 matched random sequences (gray). Y -axis values are numbers of R2ORs per 15 kb window. ( D ) Genomic distribution of the 1603 top R2ORs (red bars) versus that of 1000 sets of matched random sequences (gray bars; mean ± SD). TSS refers to −1000 to +100 bp from 5′-end of annotated RNA. Transcription Termination Site ( TTS ) is defined as −100 to +1000 bp from the 3′-end of the transcript. Inset shows blow up of TTS and TTS data.
    Chip Input Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/chip input dna/product/Illumina Inc
    Average 88 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
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    88
    abcam input control dna
    Schematic depiction of centromeric molecular alterations in cancer. Copy number alterations in the form of α-satellite deletions are observed across cancer types in both cell lines and tissue ( 50 ). <t>CENPA,</t> the H3 variant that traditionally occupies α-satellite <t>DNA,</t> ectopically binds gene regulatory elements, such as transcriptional start sites ( TSS ), of genes important for cell cycle progression, such as CDC25C , when overexpressed in cancer. Future studies are necessary to functionally link the ectopic localization to the α-satellite deletions.
    Input Control Dna, supplied by abcam, used in various techniques. Bioz Stars score: 88/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/input control dna/product/abcam
    Average 88 stars, based on 1 article reviews
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    input control dna - by Bioz Stars, 2020-08
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    85
    Illumina Inc st20 chicken input dna chip seq
    ) (A) Annotation of hNCC active enhancers. Mouse Genome Informatics (MGI) Expression Detected (red) contains information on tissue and developmental stage– specific expression in mouse; Mouse Phenotypes (blue) ontology contains data on mouse genotype-phenotype associations; Human Malformations (purple) ontology contains data on human genotype - phenotype associations. The x-axis values correspond to Binomial raw (uncorrected) p-values. (B) Dorsal anterior neural folds from st8 chicken embryos were excised (red line) and cultured ex vivo for 72 hours, resulting in emigration of NCC estimated to correspond to chicken st11-14 cranial NCC. (C) Chicken <t>st20</t> NCC were isolated in vivo from frontonasal prominences (FNP). FNPs were incubated with dispase in order to remove the surface ectoderm and forebrain neuroectoderm, which resulted in FNPs solely comprised of NCC. (D-E) Average ChIP-seq H3K27ac profiles from chicken NCC at st11-14 (D) or st20 (E) generated around central positions of hNCC enhancers conserved in the chicken genome. (F) Select overrepresented <t>DNA</t> sequence motifs enriched at hNCC active enhancers. Statistical significance (p-value) of the motifs over-representation is shown.
    St20 Chicken Input Dna Chip Seq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/st20 chicken input dna chip seq/product/Illumina Inc
    Average 85 stars, based on 1 article reviews
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    st20 chicken input dna chip seq - by Bioz Stars, 2020-08
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    Image Search Results


    Genome-wide characterization of Runx2 occupied regions (R2ORs). C4-2B/Rx2 dox cells were subjected to Runx2 ChIP-seq analysis after dox treatment and immunoprecipitation of Runx2-bound DNA fragments with anti-FLAG antibodies. ( A ) ChIP-seq results showing R2ORs upstream of the KLK and CSF2 TSS s . Raw ChIP-seq data are presented as frequency of reads per location for 30 kb of DNA sequences at the KLK2 (top) and CSF2 (bottom) loci. For each locus, the upper track shows results for chromatin aliquoted prior to immunoprecipitation (input). Regions investigated in Figure 1 by conventional ChIP assays are marked by black bars. ( B ) Sixteen Runx2 ChIP-seq peaks were validated by conventional ChIP-qPCR and the ChIP-seq scores are plotted against the qPCR enrichment factors. ( C ) Distance from the 1603 top R2ORs to the nearest TSS were mapped (red) and are shown along with control distribution patterns of 1000 sets of 1603 matched random sequences (gray). Y -axis values are numbers of R2ORs per 15 kb window. ( D ) Genomic distribution of the 1603 top R2ORs (red bars) versus that of 1000 sets of matched random sequences (gray bars; mean ± SD). TSS refers to −1000 to +100 bp from 5′-end of annotated RNA. Transcription Termination Site ( TTS ) is defined as −100 to +1000 bp from the 3′-end of the transcript. Inset shows blow up of TTS and TTS data.

    Journal: Nucleic Acids Research

    Article Title: Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion

    doi: 10.1093/nar/gkr1219

    Figure Lengend Snippet: Genome-wide characterization of Runx2 occupied regions (R2ORs). C4-2B/Rx2 dox cells were subjected to Runx2 ChIP-seq analysis after dox treatment and immunoprecipitation of Runx2-bound DNA fragments with anti-FLAG antibodies. ( A ) ChIP-seq results showing R2ORs upstream of the KLK and CSF2 TSS s . Raw ChIP-seq data are presented as frequency of reads per location for 30 kb of DNA sequences at the KLK2 (top) and CSF2 (bottom) loci. For each locus, the upper track shows results for chromatin aliquoted prior to immunoprecipitation (input). Regions investigated in Figure 1 by conventional ChIP assays are marked by black bars. ( B ) Sixteen Runx2 ChIP-seq peaks were validated by conventional ChIP-qPCR and the ChIP-seq scores are plotted against the qPCR enrichment factors. ( C ) Distance from the 1603 top R2ORs to the nearest TSS were mapped (red) and are shown along with control distribution patterns of 1000 sets of 1603 matched random sequences (gray). Y -axis values are numbers of R2ORs per 15 kb window. ( D ) Genomic distribution of the 1603 top R2ORs (red bars) versus that of 1000 sets of matched random sequences (gray bars; mean ± SD). TSS refers to −1000 to +100 bp from 5′-end of annotated RNA. Transcription Termination Site ( TTS ) is defined as −100 to +1000 bp from the 3′-end of the transcript. Inset shows blow up of TTS and TTS data.

    Article Snippet: ChIP-sequencing and peak calling Runx2 ChIP DNA along with ChIP input DNA were prepared as above from C4-2B/Rx2dox cells treated with dox for 14 h, and high throughput sequencing of the 500–1000 bp fragments was performed using Illumina Hi-Seq 2000.

    Techniques: Genome Wide, Chromatin Immunoprecipitation, Immunoprecipitation, Real-time Polymerase Chain Reaction

    DNA sequence motifs enriched in R2ORs. Motifs enriched in R2ORs compared to 1603 matched random sequences were identified using HOMER 3.1. ( A ) Logo for the top motif ( Runx2 ) is shown above the Runx1 logo identified by Pencovich et al. ( 35 ). ( B ) Motifs identified after R2ORs were re-analyzed as in A following masking of the Runx2 motifs. ( C ) Motif statistics. P- values are for motif enrichment. The percentages of R2ORs containing at least one copy of each motif are indicated against the percentage of motif-containing random sequences. Motifs/R2OR indicates for each motif the average number of copies per R2OR in R2ORs containing at least one copy.

    Journal: Nucleic Acids Research

    Article Title: Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion

    doi: 10.1093/nar/gkr1219

    Figure Lengend Snippet: DNA sequence motifs enriched in R2ORs. Motifs enriched in R2ORs compared to 1603 matched random sequences were identified using HOMER 3.1. ( A ) Logo for the top motif ( Runx2 ) is shown above the Runx1 logo identified by Pencovich et al. ( 35 ). ( B ) Motifs identified after R2ORs were re-analyzed as in A following masking of the Runx2 motifs. ( C ) Motif statistics. P- values are for motif enrichment. The percentages of R2ORs containing at least one copy of each motif are indicated against the percentage of motif-containing random sequences. Motifs/R2OR indicates for each motif the average number of copies per R2OR in R2ORs containing at least one copy.

    Article Snippet: ChIP-sequencing and peak calling Runx2 ChIP DNA along with ChIP input DNA were prepared as above from C4-2B/Rx2dox cells treated with dox for 14 h, and high throughput sequencing of the 500–1000 bp fragments was performed using Illumina Hi-Seq 2000.

    Techniques: Sequencing

    Schematic depiction of centromeric molecular alterations in cancer. Copy number alterations in the form of α-satellite deletions are observed across cancer types in both cell lines and tissue ( 50 ). CENPA, the H3 variant that traditionally occupies α-satellite DNA, ectopically binds gene regulatory elements, such as transcriptional start sites ( TSS ), of genes important for cell cycle progression, such as CDC25C , when overexpressed in cancer. Future studies are necessary to functionally link the ectopic localization to the α-satellite deletions.

    Journal: The Journal of Biological Chemistry

    Article Title: The role of the histone H3 variant CENPA in prostate cancer

    doi: 10.1074/jbc.RA119.010080

    Figure Lengend Snippet: Schematic depiction of centromeric molecular alterations in cancer. Copy number alterations in the form of α-satellite deletions are observed across cancer types in both cell lines and tissue ( 50 ). CENPA, the H3 variant that traditionally occupies α-satellite DNA, ectopically binds gene regulatory elements, such as transcriptional start sites ( TSS ), of genes important for cell cycle progression, such as CDC25C , when overexpressed in cancer. Future studies are necessary to functionally link the ectopic localization to the α-satellite deletions.

    Article Snippet: CENPA-targeted ChIP DNA and input control DNA were prepared for parallel sequencing using the TruSeq ChIP library preparation kit (Illumina) according to the manufacturer's protocol.

    Techniques: Variant Assay

    ) (A) Annotation of hNCC active enhancers. Mouse Genome Informatics (MGI) Expression Detected (red) contains information on tissue and developmental stage– specific expression in mouse; Mouse Phenotypes (blue) ontology contains data on mouse genotype-phenotype associations; Human Malformations (purple) ontology contains data on human genotype - phenotype associations. The x-axis values correspond to Binomial raw (uncorrected) p-values. (B) Dorsal anterior neural folds from st8 chicken embryos were excised (red line) and cultured ex vivo for 72 hours, resulting in emigration of NCC estimated to correspond to chicken st11-14 cranial NCC. (C) Chicken st20 NCC were isolated in vivo from frontonasal prominences (FNP). FNPs were incubated with dispase in order to remove the surface ectoderm and forebrain neuroectoderm, which resulted in FNPs solely comprised of NCC. (D-E) Average ChIP-seq H3K27ac profiles from chicken NCC at st11-14 (D) or st20 (E) generated around central positions of hNCC enhancers conserved in the chicken genome. (F) Select overrepresented DNA sequence motifs enriched at hNCC active enhancers. Statistical significance (p-value) of the motifs over-representation is shown.

    Journal: Cell stem cell

    Article Title: Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest

    doi: 10.1016/j.stem.2012.07.006

    Figure Lengend Snippet: ) (A) Annotation of hNCC active enhancers. Mouse Genome Informatics (MGI) Expression Detected (red) contains information on tissue and developmental stage– specific expression in mouse; Mouse Phenotypes (blue) ontology contains data on mouse genotype-phenotype associations; Human Malformations (purple) ontology contains data on human genotype - phenotype associations. The x-axis values correspond to Binomial raw (uncorrected) p-values. (B) Dorsal anterior neural folds from st8 chicken embryos were excised (red line) and cultured ex vivo for 72 hours, resulting in emigration of NCC estimated to correspond to chicken st11-14 cranial NCC. (C) Chicken st20 NCC were isolated in vivo from frontonasal prominences (FNP). FNPs were incubated with dispase in order to remove the surface ectoderm and forebrain neuroectoderm, which resulted in FNPs solely comprised of NCC. (D-E) Average ChIP-seq H3K27ac profiles from chicken NCC at st11-14 (D) or st20 (E) generated around central positions of hNCC enhancers conserved in the chicken genome. (F) Select overrepresented DNA sequence motifs enriched at hNCC active enhancers. Statistical significance (p-value) of the motifs over-representation is shown.

    Article Snippet: DNA libraries were prepared from hNCC p300 ChIP, hNCC FAIRE, hNCC H3K4me3 ChIP, hNCC H3K4me1 ChIP, hNCC H3K27me3 ChIP, hNCC H3K27ac ChIP, hNCC NR2F1 ChIP, hNCC NR2F2 ChIP, hNCC TFAP2A ChIP, hNCC input DNA, St11-14 Chicken H3K27ac ChIP, St20 Chicken H3K27ac ChIP, St11-14 Chicken input DNA, St20 Chicken input DNA ChIP-seq, FAIRE-seq and input libraries were prepared according to Illumina protocol and sequenced using Illumina Genome Analyzer.

    Techniques: Expressing, Cell Culture, Ex Vivo, Isolation, In Vivo, Incubation, Chromatin Immunoprecipitation, Generated, Sequencing, Significance Assay