human cot-1 dna Search Results


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    Thermo Fisher human cot1 dna
    The human Xi is partially reactivated upon cell fusion-mediated reprogramming. ( a ) Expression of human Xi transcripts examined by allele-specific RNA-seq in female human fibroblasts (clone b1) before (day 0) and after (day 5/6) mESC-fusion. Data points show Xi expression of 113 genes along the X chromosome ( x axis) where genes that escape XCI before reprogramming (blue closed circles),, or that are sensitive to reactivation following fusion (day 5 green open circles; day 6 green closed circles) are highlighted. Xi expression is represented as the ratio of reads overlapping the minor (Xi) allele versus the total of both alleles (Xi+Xa) and result from two biological replicates. Genes were classified accordingly to Xi expression ratio and significance 62 , as detailed in the Methods. ( b ) RNA-FISH analyses of candidate reactivation-refractory ( HDAC8 ) and reactivation-sensitive ( RP11-706O15.1 , WWC3 ) genes in human fibroblasts before (day 0) and after mESC-fusion (day 5). Histogram plots show the percentage of human nuclei (heterokaryon/hybrid cells; n = 44/83, 33/74, 48/81 for HDAC8 , RP11-706O15.1 and WWC3 , respectively) with one, two, or > 2 punctate RNA signals. Representative confocal images showing mono-allelic expression of WWC3 (red) in human nuclei before (day 0) and bi-allelic expression after (day 5) mESC-fusion (arrowed) where mouse nuclei were discriminated using mCotI probe (green). Arrows indicate transcribed loci (that is, punctate RNA signals). Scale bar, 5 μm. ( c ) Confocal images of hFxmESC heterokaryons where either one (top) or two (lower) transcribed X chromosomes (arrowed) were evident. Mouse <t>Cot1</t> probe identifies mouse (ESC-derived) nuclei. X chr RNA paints were pre-treated with human Cot1 <t>DNA</t> to diminish the detection of repeat-rich elements 63 within the transcribed X chromosome domains. Xa* marks the smaller (and Xa the larger) domain. Scale bar, 5 μm. ( d ) Box plots showing the volume of the RNA (top) and DNA (bottom) X domains detected by sequential RNA/DNA FISH in hFxmESC expressing one (single domain) or two (two domains) X chromosomes (shown in Supplementary Fig. 5b ). Significant volume differences are highlighted ( P values) and were estimated by Wilcoxon signed-rank test or Mann–Whitney test, for the comparison of Xa/Xa* and Xa/Xi, respectively. Data represent at least 50 cells in each graph. See also Supplementary Fig. 5 .
    Human Cot1 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 868 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human cot1 dna/product/Thermo Fisher
    Average 99 stars, based on 868 article reviews
    Price from $9.99 to $1999.99
    human cot1 dna - by Bioz Stars, 2020-08
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    92
    Millipore human cot 1 dna
    The human Xi is partially reactivated upon cell fusion-mediated reprogramming. ( a ) Expression of human Xi transcripts examined by allele-specific RNA-seq in female human fibroblasts (clone b1) before (day 0) and after (day 5/6) mESC-fusion. Data points show Xi expression of 113 genes along the X chromosome ( x axis) where genes that escape XCI before reprogramming (blue closed circles),, or that are sensitive to reactivation following fusion (day 5 green open circles; day 6 green closed circles) are highlighted. Xi expression is represented as the ratio of reads overlapping the minor (Xi) allele versus the total of both alleles (Xi+Xa) and result from two biological replicates. Genes were classified accordingly to Xi expression ratio and significance 62 , as detailed in the Methods. ( b ) RNA-FISH analyses of candidate reactivation-refractory ( HDAC8 ) and reactivation-sensitive ( RP11-706O15.1 , WWC3 ) genes in human fibroblasts before (day 0) and after mESC-fusion (day 5). Histogram plots show the percentage of human nuclei (heterokaryon/hybrid cells; n = 44/83, 33/74, 48/81 for HDAC8 , RP11-706O15.1 and WWC3 , respectively) with one, two, or > 2 punctate RNA signals. Representative confocal images showing mono-allelic expression of WWC3 (red) in human nuclei before (day 0) and bi-allelic expression after (day 5) mESC-fusion (arrowed) where mouse nuclei were discriminated using mCotI probe (green). Arrows indicate transcribed loci (that is, punctate RNA signals). Scale bar, 5 μm. ( c ) Confocal images of hFxmESC heterokaryons where either one (top) or two (lower) transcribed X chromosomes (arrowed) were evident. Mouse <t>Cot1</t> probe identifies mouse (ESC-derived) nuclei. X chr RNA paints were pre-treated with human Cot1 <t>DNA</t> to diminish the detection of repeat-rich elements 63 within the transcribed X chromosome domains. Xa* marks the smaller (and Xa the larger) domain. Scale bar, 5 μm. ( d ) Box plots showing the volume of the RNA (top) and DNA (bottom) X domains detected by sequential RNA/DNA FISH in hFxmESC expressing one (single domain) or two (two domains) X chromosomes (shown in Supplementary Fig. 5b ). Significant volume differences are highlighted ( P values) and were estimated by Wilcoxon signed-rank test or Mann–Whitney test, for the comparison of Xa/Xa* and Xa/Xi, respectively. Data represent at least 50 cells in each graph. See also Supplementary Fig. 5 .
    Human Cot 1 Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 92/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human cot 1 dna/product/Millipore
    Average 92 stars, based on 37 article reviews
    Price from $9.99 to $1999.99
    human cot 1 dna - by Bioz Stars, 2020-08
    92/100 stars
      Buy from Supplier

    92
    Thermo Fisher •human cot1 dna
    Principle of array-CGH. Genomic <t>DNA</t> from two cell populations is differentially labeled and hybridized to a microarray in the presence of <t>Cot1</t> DNA to suppress repeat sequences. The fluorescent ratios on each array spot are calculated and normalized so
    •Human Cot1 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/•human cot1 dna/product/Thermo Fisher
    Average 92 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    •human cot1 dna - by Bioz Stars, 2020-08
    92/100 stars
      Buy from Supplier

    Image Search Results


    The human Xi is partially reactivated upon cell fusion-mediated reprogramming. ( a ) Expression of human Xi transcripts examined by allele-specific RNA-seq in female human fibroblasts (clone b1) before (day 0) and after (day 5/6) mESC-fusion. Data points show Xi expression of 113 genes along the X chromosome ( x axis) where genes that escape XCI before reprogramming (blue closed circles),, or that are sensitive to reactivation following fusion (day 5 green open circles; day 6 green closed circles) are highlighted. Xi expression is represented as the ratio of reads overlapping the minor (Xi) allele versus the total of both alleles (Xi+Xa) and result from two biological replicates. Genes were classified accordingly to Xi expression ratio and significance 62 , as detailed in the Methods. ( b ) RNA-FISH analyses of candidate reactivation-refractory ( HDAC8 ) and reactivation-sensitive ( RP11-706O15.1 , WWC3 ) genes in human fibroblasts before (day 0) and after mESC-fusion (day 5). Histogram plots show the percentage of human nuclei (heterokaryon/hybrid cells; n = 44/83, 33/74, 48/81 for HDAC8 , RP11-706O15.1 and WWC3 , respectively) with one, two, or > 2 punctate RNA signals. Representative confocal images showing mono-allelic expression of WWC3 (red) in human nuclei before (day 0) and bi-allelic expression after (day 5) mESC-fusion (arrowed) where mouse nuclei were discriminated using mCotI probe (green). Arrows indicate transcribed loci (that is, punctate RNA signals). Scale bar, 5 μm. ( c ) Confocal images of hFxmESC heterokaryons where either one (top) or two (lower) transcribed X chromosomes (arrowed) were evident. Mouse Cot1 probe identifies mouse (ESC-derived) nuclei. X chr RNA paints were pre-treated with human Cot1 DNA to diminish the detection of repeat-rich elements 63 within the transcribed X chromosome domains. Xa* marks the smaller (and Xa the larger) domain. Scale bar, 5 μm. ( d ) Box plots showing the volume of the RNA (top) and DNA (bottom) X domains detected by sequential RNA/DNA FISH in hFxmESC expressing one (single domain) or two (two domains) X chromosomes (shown in Supplementary Fig. 5b ). Significant volume differences are highlighted ( P values) and were estimated by Wilcoxon signed-rank test or Mann–Whitney test, for the comparison of Xa/Xa* and Xa/Xi, respectively. Data represent at least 50 cells in each graph. See also Supplementary Fig. 5 .

    Journal: Nature Communications

    Article Title: Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming

    doi: 10.1038/ncomms12354

    Figure Lengend Snippet: The human Xi is partially reactivated upon cell fusion-mediated reprogramming. ( a ) Expression of human Xi transcripts examined by allele-specific RNA-seq in female human fibroblasts (clone b1) before (day 0) and after (day 5/6) mESC-fusion. Data points show Xi expression of 113 genes along the X chromosome ( x axis) where genes that escape XCI before reprogramming (blue closed circles),, or that are sensitive to reactivation following fusion (day 5 green open circles; day 6 green closed circles) are highlighted. Xi expression is represented as the ratio of reads overlapping the minor (Xi) allele versus the total of both alleles (Xi+Xa) and result from two biological replicates. Genes were classified accordingly to Xi expression ratio and significance 62 , as detailed in the Methods. ( b ) RNA-FISH analyses of candidate reactivation-refractory ( HDAC8 ) and reactivation-sensitive ( RP11-706O15.1 , WWC3 ) genes in human fibroblasts before (day 0) and after mESC-fusion (day 5). Histogram plots show the percentage of human nuclei (heterokaryon/hybrid cells; n = 44/83, 33/74, 48/81 for HDAC8 , RP11-706O15.1 and WWC3 , respectively) with one, two, or > 2 punctate RNA signals. Representative confocal images showing mono-allelic expression of WWC3 (red) in human nuclei before (day 0) and bi-allelic expression after (day 5) mESC-fusion (arrowed) where mouse nuclei were discriminated using mCotI probe (green). Arrows indicate transcribed loci (that is, punctate RNA signals). Scale bar, 5 μm. ( c ) Confocal images of hFxmESC heterokaryons where either one (top) or two (lower) transcribed X chromosomes (arrowed) were evident. Mouse Cot1 probe identifies mouse (ESC-derived) nuclei. X chr RNA paints were pre-treated with human Cot1 DNA to diminish the detection of repeat-rich elements 63 within the transcribed X chromosome domains. Xa* marks the smaller (and Xa the larger) domain. Scale bar, 5 μm. ( d ) Box plots showing the volume of the RNA (top) and DNA (bottom) X domains detected by sequential RNA/DNA FISH in hFxmESC expressing one (single domain) or two (two domains) X chromosomes (shown in Supplementary Fig. 5b ). Significant volume differences are highlighted ( P values) and were estimated by Wilcoxon signed-rank test or Mann–Whitney test, for the comparison of Xa/Xa* and Xa/Xi, respectively. Data represent at least 50 cells in each graph. See also Supplementary Fig. 5 .

    Article Snippet: Briefly, 5 μl of concentrated X paint was mixed with 5 μg of human Cot1 DNA (Life Technologies), denatured for 7 min at 75 °C and pre-annealed for 30 min at 37 °C in order to deplete the probe of Cot1 repeats before hybridizing with cells overnight at 37 °C.

    Techniques: Expressing, RNA Sequencing Assay, Fluorescence In Situ Hybridization, Derivative Assay, MANN-WHITNEY

    FISH analyses of the HAC with the PAC in CHO cells and MSCs . FISH analyses of CHO (21HAC2- hgf , gdnf , igf-1 , e-luc ) and MSCs (21HAC2- hgf , gdnf , igf-1 , e-luc ). Digoxigenin-labeled human COT-1 DNA (red) and p11-4 (red) were used to detect the ( a ) HAC in CHO cells and ( b ) MSCs, respectively. Biotin-labeled PAC (green) was used to detect the PAC DNA on the HAC in a and b . Chromosomal DNA was counterstained with 4′,6-diamidino-2-phenylindole. The inset shows an enlarged image of the HAC with the PAC (arrow).

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Use of a Human Artificial Chromosome for Delivering Trophic Factors in a Rodent Model of Amyotrophic Lateral Sclerosis

    doi: 10.1038/mtna.2015.28

    Figure Lengend Snippet: FISH analyses of the HAC with the PAC in CHO cells and MSCs . FISH analyses of CHO (21HAC2- hgf , gdnf , igf-1 , e-luc ) and MSCs (21HAC2- hgf , gdnf , igf-1 , e-luc ). Digoxigenin-labeled human COT-1 DNA (red) and p11-4 (red) were used to detect the ( a ) HAC in CHO cells and ( b ) MSCs, respectively. Biotin-labeled PAC (green) was used to detect the PAC DNA on the HAC in a and b . Chromosomal DNA was counterstained with 4′,6-diamidino-2-phenylindole. The inset shows an enlarged image of the HAC with the PAC (arrow).

    Article Snippet: FISH analyses were performed using fixed metaphase spreads of each cell hybrid using digoxigenin-labeled (Roche, Basel, Switzerland) human COT-1 DNA (Invitrogen), digoxigenin-labeled p11-4 (hChr.21-derived alpha-satellite clone), and biotin-labeled PAC DNA, essentially as described previously.

    Techniques: Fluorescence In Situ Hybridization, HAC Assay, Labeling

    Optimizing the X-chromosome paint RNA FISH. 5 μl of cy3-X-chromosome paint are co-precipitated with various amounts of human Cot-1 DNA prior to over-night hybridisation. Optimization of the quantity of Cot-1 should be performed when changing supplier for chromosome paint.

    Journal: Bio-protocol

    Article Title: Single-cell Visualization of Chromosome Transcriptional Territories by RNA-paint

    doi: 10.21769/BioProtoc.1914

    Figure Lengend Snippet: Optimizing the X-chromosome paint RNA FISH. 5 μl of cy3-X-chromosome paint are co-precipitated with various amounts of human Cot-1 DNA prior to over-night hybridisation. Optimization of the quantity of Cot-1 should be performed when changing supplier for chromosome paint.

    Article Snippet: 24-well plates (Sigma-Aldrich, catalog number: Z707791-126EA) 13 mm round coverslips (Thermo Fisher Scientific, catalog number: 174950) Glass slides Filter (0.2 μm) Filtration unit (Merck Millipore, catalog number: SCGPS05RE) Human embryonic stem cells (H9, WIBR2 and HUES1) and cancer cells (TCCSUP and RT112) Matrigel PBS solution (Life Technologies) Sodium chloride (NaCl) (Sigma-Aldrich, catalog number: S7653) Sucrose (Sigma-Aldrich, catalog number: S0389) Magnesium chloride (MgCl2 ) (Sigma-Aldrich, catalog number: M8266) PIPES (Sigma-Aldrich, catalog number: P6757) NaOH Triton X-100 (Sigma-Aldrich, catalog number: X100) Ribonucleoside vanadyl complex (New England Biolabs, catalog number: S1402) Paraformaldehyde (PFA) (16%, EM grade) (VWR International, catalog number: 100503-916) EtOH Human Cot-1 DNA (Life Technologies) Sodium acetate anhydrous (NaOAc) (Sigma-Aldrich, catalog number: W302406) Deionized formamide (Sigma-Aldrich, catalog number: F9037) Rubber cement 20x SSC (Sigma-Aldrich, catalog number: 93017) 20 mg/ml BSA (New England Biolabs, catalog number: B9000S) Dextran sulfate (Sigma-Aldrich, catalog number: 67578) Formamide (Sigma-Aldrich, catalog number: 47670) Mounting medium (Vector Laboratories, catalog number: H-1200) Cy3-labelled human X-Chromosome paint (Metasystem, catalog number: D-0323-050-OR) FITC-labelled human X-Chromosome paint (Metasystem, catalog number: D-0323-050-FI) CSK buffer (see ) 3% PFA/PBS solution (see ) Hybridisation buffer (2x) (see ) Washing solution (50% formamide/2x SSC) (see ) Denaturating solution (70% formamide/2x SSC) (see )

    Techniques: Fluorescence In Situ Hybridization, Hybridization

    hMSCs are retained and proliferate in the right ventricle (RV). Double immunofluorescence staining of RV sections for (A) 4′-6-diamidino-2-phenylindole (DAPI) for nuclear staining (blue) and Ki67 (green), (B) CD105 (red) from PV-banded pigs 24 days after intracoronary injection of hMSCs. (C) Merged sections show co-localization of CD105 and Ki67, indicating proliferation of hMSCs. Arrows show positive immunostaining. Representative images are shown. FISH was performed on RV sections to confirm the presence of human cells. (E) Human control hybridized with combined green (human) and red (pig) species-specific Cot-1 FISH probe. (F) Two adjacent human (daughter) cells in the final stages of cell division (telophase/cytokinesis). (G) An individual human cell (green) and (H) a group of human cells (green) are seen in the RV. Representative images are shown.

    Journal: Cytotherapy

    Article Title: Persistence and proliferation of human mesenchymal stromal cells in the right ventricular myocardium after intracoronary injection in a large animal model of pulmonary hypertension

    doi: 10.1016/j.jcyt.2017.03.002

    Figure Lengend Snippet: hMSCs are retained and proliferate in the right ventricle (RV). Double immunofluorescence staining of RV sections for (A) 4′-6-diamidino-2-phenylindole (DAPI) for nuclear staining (blue) and Ki67 (green), (B) CD105 (red) from PV-banded pigs 24 days after intracoronary injection of hMSCs. (C) Merged sections show co-localization of CD105 and Ki67, indicating proliferation of hMSCs. Arrows show positive immunostaining. Representative images are shown. FISH was performed on RV sections to confirm the presence of human cells. (E) Human control hybridized with combined green (human) and red (pig) species-specific Cot-1 FISH probe. (F) Two adjacent human (daughter) cells in the final stages of cell division (telophase/cytokinesis). (G) An individual human cell (green) and (H) a group of human cells (green) are seen in the RV. Representative images are shown.

    Article Snippet: A two-color species-differentiation fluorescence in situ hybridization (FISH) probe was generated by nick translation of species-specific repeated DNA sequences: human Cot-1 (Invitrogen) was labeled with SpectrumGreen, and porcine ID Block-It Cot-1 (Empire Genomics) was labeled with SpectrumOrange.

    Techniques: Double Immunofluorescence Staining, Staining, Injection, Immunostaining, Fluorescence In Situ Hybridization

    XIST RNA cloud paints an active X chromosome in MCF7 nuclei. A) DNA FISH using the single Xq22.3 locus RP11-349A16 probe (red), and X alpha-satellite probe (green). Cell populations with three Xs display two different hybridization patterns: two Xs with a single red spot (white arrows) and a chromosome with two red signals (red arrow). B) Simultaneous detection of XIST RNA (green), X chromosome territory (blue) and Xq22.3 locus (red). The X chromosome expressing XIST has one copy of the RP11-349A16 region (merge). C) Replication timing analysis. MCF7 and HMEC were briefly labelled with BrdU and analyzed by DNA FISH using the single Xq22.3 locus RP11-349A16 probe and by BrdU immunofluorescence. The pattern of FISH staining seen in BrdU-positive cells was scored for at least 300 nuclei of each cell type: nuclei with only “singlets” are those in which no Xs has yet replicated; nuclei with “singlet/s+doublet/s” pattern contain unreplicated and replicated Xs; nuclei with only “doublets” have all replicated Xs. Both MCF7 subpopulations with two and three Xs display a synchronous replication timing. D) Characterisation of the chromatin signatures of XIST-positive X chromosome in MCF7 and HMEC, by simultaneous FISH detection of XIST RNA (red) and Cot-1 RNA (green); DAPI nuclear staining is in blue. A line scan of fluorescence intensity (white bars) is shown for both cell types. In HMEC, the scan plot revealed overlap of the DAPI and XIST RNA signals, whereas the Cot-1 RNA signal is depleted, as expected for an inactive X chromosome. On the contrary, in MCF7 cells the line scan through the XIST-positive territory shows high intensity of the Cot-1 RNA signal combined with low DAPI intensity, typical signs of euchromatin.

    Journal: PLoS ONE

    Article Title: Misbehaviour of XIST RNA in Breast Cancer Cells

    doi: 10.1371/journal.pone.0005559

    Figure Lengend Snippet: XIST RNA cloud paints an active X chromosome in MCF7 nuclei. A) DNA FISH using the single Xq22.3 locus RP11-349A16 probe (red), and X alpha-satellite probe (green). Cell populations with three Xs display two different hybridization patterns: two Xs with a single red spot (white arrows) and a chromosome with two red signals (red arrow). B) Simultaneous detection of XIST RNA (green), X chromosome territory (blue) and Xq22.3 locus (red). The X chromosome expressing XIST has one copy of the RP11-349A16 region (merge). C) Replication timing analysis. MCF7 and HMEC were briefly labelled with BrdU and analyzed by DNA FISH using the single Xq22.3 locus RP11-349A16 probe and by BrdU immunofluorescence. The pattern of FISH staining seen in BrdU-positive cells was scored for at least 300 nuclei of each cell type: nuclei with only “singlets” are those in which no Xs has yet replicated; nuclei with “singlet/s+doublet/s” pattern contain unreplicated and replicated Xs; nuclei with only “doublets” have all replicated Xs. Both MCF7 subpopulations with two and three Xs display a synchronous replication timing. D) Characterisation of the chromatin signatures of XIST-positive X chromosome in MCF7 and HMEC, by simultaneous FISH detection of XIST RNA (red) and Cot-1 RNA (green); DAPI nuclear staining is in blue. A line scan of fluorescence intensity (white bars) is shown for both cell types. In HMEC, the scan plot revealed overlap of the DAPI and XIST RNA signals, whereas the Cot-1 RNA signal is depleted, as expected for an inactive X chromosome. On the contrary, in MCF7 cells the line scan through the XIST-positive territory shows high intensity of the Cot-1 RNA signal combined with low DAPI intensity, typical signs of euchromatin.

    Article Snippet: Cot-1 probe was obtained labeling 100 ng of Cot-1 DNA (1 mg/ml, Invitrogen) by Prime-It Fluor, Fluorescence labeling Kit with FITC-dUTP.

    Techniques: Fluorescence In Situ Hybridization, Hybridization, Expressing, Immunofluorescence, Staining, Fluorescence

    Array fabrication and gene annotation (A) False-colour image generated from a bovine-Cy5, human-Cy3 hybridisation. False colour images were generated using the programme ScanAlyze, version 2.44 . The full array (24 × 25 spotting pattern) consists of 16 blocks with each gene spotted 5 times per block therefore 80 potential data points present for expression analysis per gene. A blow-up of 4 blocks illustrating the Chip design is presented. The ACTIN cDNAs acting as guide-dots can be seen as intense yellow spots demarcating each block. In addition, the majority of spots appear yellow due to similar expression levels of the orthologous genes. (B) Functional annotation of the 349 genes as set out by the Gene Ontology Consortium .The proportion of these genes within each functional / biological annotation is represented on the Y-axis and the annotation on the X-axis. (C) Chromosomal distribution of the 349 genes. The number of genes within each chromosome is represented on the Y-axis and the chromosome numbers on the X-axis.

    Journal: BMC Genomics

    Article Title: Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays

    doi: 10.1186/1471-2164-5-83

    Figure Lengend Snippet: Array fabrication and gene annotation (A) False-colour image generated from a bovine-Cy5, human-Cy3 hybridisation. False colour images were generated using the programme ScanAlyze, version 2.44 . The full array (24 × 25 spotting pattern) consists of 16 blocks with each gene spotted 5 times per block therefore 80 potential data points present for expression analysis per gene. A blow-up of 4 blocks illustrating the Chip design is presented. The ACTIN cDNAs acting as guide-dots can be seen as intense yellow spots demarcating each block. In addition, the majority of spots appear yellow due to similar expression levels of the orthologous genes. (B) Functional annotation of the 349 genes as set out by the Gene Ontology Consortium .The proportion of these genes within each functional / biological annotation is represented on the Y-axis and the annotation on the X-axis. (C) Chromosomal distribution of the 349 genes. The number of genes within each chromosome is represented on the Y-axis and the chromosome numbers on the X-axis.

    Article Snippet: After concentrating cDNAs by evaporation in a SpeedVac, labelled targets were resuspended in 20 μl of hybridisation buffer (10 μg polydA and 20 μg Human Cot1 DNA,-Invitrogen; DIG-Easy Hybridisation mix -Roche).

    Techniques: Generated, Hybridization, Blocking Assay, Expressing, Chromatin Immunoprecipitation, Functional Assay

    Principle of array-CGH. Genomic DNA from two cell populations is differentially labeled and hybridized to a microarray in the presence of Cot1 DNA to suppress repeat sequences. The fluorescent ratios on each array spot are calculated and normalized so

    Journal:

    Article Title: Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes

    doi: 10.1038/nprot.2007.53

    Figure Lengend Snippet: Principle of array-CGH. Genomic DNA from two cell populations is differentially labeled and hybridized to a microarray in the presence of Cot1 DNA to suppress repeat sequences. The fluorescent ratios on each array spot are calculated and normalized so

    Article Snippet: •2× TY medium, pH 7.4 (see REAGENT SETUP) •Solution I (see REAGENT SETUP) •Solution II (see REAGENT SETUP) •Solution III (see REAGENT SETUP) •Isopropanol •70% ethanol •100% ethanol •80% ethanol •T0.1E solution, pH 8 (see REAGENT SETUP) •RNaseA (ICN Biochemicals, cat. no. 101076) •DOP-PCR primers: •DOP 1: 5′ CCGACTCGAGNNNNNNCTAGAA 3′ •DOP 2: 5′ CCGACTCGAGNNNNNNTAGGAG 3′ •DOP 3: 5′ CCGACTCGAGNNNNNNTTCTAG 3′ •TAPS ( N -[tris(hydroxymethyl)methyl]-3-aminopropanesulfonic acid (Sigma-Aldrich, cat. no. T5130) •TAPS salt solution (see REAGENT SETUP) •TAPS2 buffer (see REAGENT SETUP) •Amino-linked primer: •5′ GGAAACAGCCCGACTCGAG 3′ •Amplitaq polymerase, 5 U μl−1 (Roche, cat. no. N808-0145) •dNTPs (Amersham Biosciences, cat. no. 27-2035-01) •Amino-linking buffer (see REAGENT SETUP) •4× microarray spotting buffer: 1 M sodium phosphate buffer, pH 8.5, 0.001% sarkosyl •1% (w/v) ammonium hydroxide solution (prepared with HPLC water) •0.1% (w/v) sodium dodecyl sulfate solution (prepared with HPLC water) •HPCL water •BioPrime Labeling Kit (Invitrogen, cat. no. 18094011) •10× dNTP mix (1 mM dCTP, 2 mM dATP, 2 mM dGTP, 2 mM dTTP in TE buffer) •1 mM Cy3-dCTP (NEN Life Science, cat. no. NEL 576) •1 mM Cy5-dCTP (NEN Life Science, cat. no. NEL 577) •Manual array hybridization buffer (see REAGENT SETUP) •3 M NaAc, pH 5.2 •Human Cot1 DNA (Invitrogen, cat. no. 15279-101) •20% formamide solution •50% formamide/2× SSC •PBS/0.05% Tween 20 •Automated array pre/hybridization buffer (see REAGENT SETUP) •Herring sperm DNA (Sigma, cat. no. D7290) •0.1× SSC •PBS/0.05% Tween 20/2 mM cysteamine •Cysteamine (Sigma, cat. no. M9768)

    Techniques: Labeling, Microarray