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  • 92
    Agilent technologies array cgh analysis
    Molecular characterization of the <t>22q13.2</t> terminal deletion in subject P20. A, Magnified view of the aligned breakpoint boundaries detected by <t>array-CGH</t> analysis using an oligonucleotide-based custom 22q13 microarray (top) and a 180k Agilent kit (bottom); the deleted regions are shaded in blue. Arrowheads delimit two mosaic-deleted regions: the BP1–BP2 deletion region (from 42406240 to 42603381 bp) has an average log ratio of −0.3; the BP2–BP3 deletion region (from 42603381 to 42726895 bp) has an average log ratio of −0.5; the deleted region between BP3 and the telomere (from 42726895 to the end of chromosome 22) has an average log ratio of −0.8. The aligned UCSC map (hg18) is depicted at the bottom. The red bar indicates the map position of the RP11-141N8 BAC clone we used to confirm by FISH the mosaicism of the BP1–BP2 region. All genes (blue bars) mapping within the BP1–BP3 regions are shown. B, FISH analysis using the RP11-141N8 clone confirms a mosaic deletion of the BP1–BP2 region revealing: (top) the presence of hybridization signals (green signal) on only one chromosome 22 (arrowhead) in 30% of the metaphases analyzed; (bottom) the presence of hybridization signals (green signals) on both chromosome 22 homologues in the remaining 70% of the metaphases analyzed (bottom). C, Tel-ACP amplification and direct sequencing of the amplified fragments revealed the breakpoint junctions at BP1, BP2 and BP3. A telomere repeat is present at all three breakpoints.
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    Agilent technologies cgh analysis
    <t>cDNA</t> microarray-based <t>CGH</t> analysis of chromosome 8q in BRCAx subgroups. Average copy number ratios for group A (yellow) and group B (blue) are shown for clones on chromosome 8q. The position of the clones on chromosome 8 is shown in Mbs from the 8p telomere, as given by alignment to the draft human genome sequence (see Materials and Methods ). Seventeen clones on 8q24 that were found to be different (α
    Cgh Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies comparative genomic hybridization cgh analysis
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
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    Agilent technologies array comparative genomic hybridization array cgh analysis
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Array Comparative Genomic Hybridization Array Cgh Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies cgh microarray analysis
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
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    Agilent technologies whole genome array cgh analysis
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Whole Genome Array Cgh Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MetaSystems cgh analysis software
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Cgh Analysis Software, supplied by MetaSystems, used in various techniques. Bioz Stars score: 88/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Abbott Laboratories cgh analysis software
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Cgh Analysis Software, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 88/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies cgh analysis software
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Cgh Analysis Software, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies array cgh analysis genomic copy number analysis
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
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    GenomeDx array cgh analysis
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Array Cgh Analysis, supplied by GenomeDx, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies cgh data analysis protocol
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Cgh Data Analysis Protocol, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Signature Genomic Laboratories, LLC custom oligonucleotide array cgh analysis software
    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , <t>Microarray</t> <t>CGH</t> profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .
    Custom Oligonucleotide Array Cgh Analysis Software, supplied by Signature Genomic Laboratories, LLC, used in various techniques. Bioz Stars score: 80/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies snp cgh array analysis
    Y MAP visualization of <t>SNP-CGH</t> data for three T1FH clones. The copy numbers and SNP-allele ratios of all three T1FH samples were visualized with Y MAP ( 49 ). Changes in the copy number estimate for regions relative to the parental strain are illustrated by dark bars drawn up- or downward, depending on the direction and magnitude of the change. These strains appear to be tetraploid on the basis of the copy number estimates for Chr7 (and most of ChrR in clone T1FHb), which are 3/4 of the other chromosomes. Color illustrates SNP status across regions. Heterozygous regions are gray, white regions do not have SNPs in the SC5314 reference sequence, and cyan is homozygous “a” alleles (e.g., aaaa on Chr5 in all three clones and ChrR in T1FHa and T1FHc and aaa in T1FHb). Intermediate ratios are indicated by intermediate colors. Blue shade represents more copies of “a” alleles (e.g., aab on the central trisomic region of ChrR in T1FHb), and purple shade represents more copies of the “b” alleles (e.g., abb on Chr7 in all three clones). The portion of ChrR in clone T1FHb to the right of the rDNA region (blue dot) is present in five copies. Major repeat sequences are represented by black dots.
    Snp Cgh Array Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies 180k agilent cgh array analysis
    Representative TCR rearrangements in ALCL as detected by Gene Scan PCR and <t>CGH.</t> ( a ) During normal T cell development, rearrangement of TCR genes occurs in a temporal manner whereby rearrangement of δ precedes γ, which is followed by β and then α, the latter of which coincides with deletion of the δ locus. DP, double positive; ISP, intermediate single positive; SP, single positive. ( b ) Typical PCR from DNA (γ, β, δ) or RNA (α) depicting the presence/absence and type of clonal rearrangements for each of the four TCR categories identified are shown, as are <t>Agilent</t> <t>180K</t> CGH TCRα/δ profiles. ( c ) Three examples representing the range of CGH TCRβ V-J rearrangements observed among the TCRαβ cases: absent (12 out of 17), oligoclonal (2 out of 17) or clonal (3 out of 17). ( d ) The percentage of human ALCL categorized as having either TCR germ line (GL), TCRαβ (TCR AB), TCRγδ (TCR GD) or TCRγ only (TCR G) rearrangements. ND, not determined.
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    Agilent technologies 44k whole human genome cgh analysis
    Representative TCR rearrangements in ALCL as detected by Gene Scan PCR and <t>CGH.</t> ( a ) During normal T cell development, rearrangement of TCR genes occurs in a temporal manner whereby rearrangement of δ precedes γ, which is followed by β and then α, the latter of which coincides with deletion of the δ locus. DP, double positive; ISP, intermediate single positive; SP, single positive. ( b ) Typical PCR from DNA (γ, β, δ) or RNA (α) depicting the presence/absence and type of clonal rearrangements for each of the four TCR categories identified are shown, as are <t>Agilent</t> <t>180K</t> CGH TCRα/δ profiles. ( c ) Three examples representing the range of CGH TCRβ V-J rearrangements observed among the TCRαβ cases: absent (12 out of 17), oligoclonal (2 out of 17) or clonal (3 out of 17). ( d ) The percentage of human ALCL categorized as having either TCR germ line (GL), TCRαβ (TCR AB), TCRγδ (TCR GD) or TCRγ only (TCR G) rearrangements. ND, not determined.
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    Agilent technologies 60k array cgh analysis
    a Overview of 1 Mb at 20q13.13 chromosome region with five reported overlapping deletions in medical literature: Decipher309, Decipher265392, Decipher257542, Decipher258702, Patient01975-5515, and index-patient. Gray shadow highlights the smallest region of overlap (SRO); the proband carried the smallest 63 kb deletion at 20q13.13 chromosome region harboring two genes ADNP and DPM1 . The ADNP gene in Helsmoortel–van der Aa syndrome is highlighted in yellow. b <t>60K</t> <t>array-CGH</t> showed a 63 kb interstitial deletion at chromosome 20q13.13 containing ADNP and DPM1 . c Quantitative real-time PCR showed that the deletion occurred de novo in the proband with primers in exons 1 and 5 of ADNP gene (index-patient: purple color; mother: pink color; father: blue color; pool of male control: light blue color; pool of female control: yellow color)
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    Image Search Results


    Molecular characterization of the 22q13.2 terminal deletion in subject P20. A, Magnified view of the aligned breakpoint boundaries detected by array-CGH analysis using an oligonucleotide-based custom 22q13 microarray (top) and a 180k Agilent kit (bottom); the deleted regions are shaded in blue. Arrowheads delimit two mosaic-deleted regions: the BP1–BP2 deletion region (from 42406240 to 42603381 bp) has an average log ratio of −0.3; the BP2–BP3 deletion region (from 42603381 to 42726895 bp) has an average log ratio of −0.5; the deleted region between BP3 and the telomere (from 42726895 to the end of chromosome 22) has an average log ratio of −0.8. The aligned UCSC map (hg18) is depicted at the bottom. The red bar indicates the map position of the RP11-141N8 BAC clone we used to confirm by FISH the mosaicism of the BP1–BP2 region. All genes (blue bars) mapping within the BP1–BP3 regions are shown. B, FISH analysis using the RP11-141N8 clone confirms a mosaic deletion of the BP1–BP2 region revealing: (top) the presence of hybridization signals (green signal) on only one chromosome 22 (arrowhead) in 30% of the metaphases analyzed; (bottom) the presence of hybridization signals (green signals) on both chromosome 22 homologues in the remaining 70% of the metaphases analyzed (bottom). C, Tel-ACP amplification and direct sequencing of the amplified fragments revealed the breakpoint junctions at BP1, BP2 and BP3. A telomere repeat is present at all three breakpoints.

    Journal: PLoS Genetics

    Article Title: Molecular Mechanisms Generating and Stabilizing Terminal 22q13 Deletions in 44 Subjects with Phelan/McDermid Syndrome

    doi: 10.1371/journal.pgen.1002173

    Figure Lengend Snippet: Molecular characterization of the 22q13.2 terminal deletion in subject P20. A, Magnified view of the aligned breakpoint boundaries detected by array-CGH analysis using an oligonucleotide-based custom 22q13 microarray (top) and a 180k Agilent kit (bottom); the deleted regions are shaded in blue. Arrowheads delimit two mosaic-deleted regions: the BP1–BP2 deletion region (from 42406240 to 42603381 bp) has an average log ratio of −0.3; the BP2–BP3 deletion region (from 42603381 to 42726895 bp) has an average log ratio of −0.5; the deleted region between BP3 and the telomere (from 42726895 to the end of chromosome 22) has an average log ratio of −0.8. The aligned UCSC map (hg18) is depicted at the bottom. The red bar indicates the map position of the RP11-141N8 BAC clone we used to confirm by FISH the mosaicism of the BP1–BP2 region. All genes (blue bars) mapping within the BP1–BP3 regions are shown. B, FISH analysis using the RP11-141N8 clone confirms a mosaic deletion of the BP1–BP2 region revealing: (top) the presence of hybridization signals (green signal) on only one chromosome 22 (arrowhead) in 30% of the metaphases analyzed; (bottom) the presence of hybridization signals (green signals) on both chromosome 22 homologues in the remaining 70% of the metaphases analyzed (bottom). C, Tel-ACP amplification and direct sequencing of the amplified fragments revealed the breakpoint junctions at BP1, BP2 and BP3. A telomere repeat is present at all three breakpoints.

    Article Snippet: C, details of the of array-CGH analysis using an oligonucleotide-based 22q13 custom array (eArray, Agilent) showing the breakpoint regions on chromosome 22q (left) and 12q (right) in cases P15/P16.

    Techniques: Microarray, BAC Assay, Fluorescence In Situ Hybridization, Hybridization, Amplification, Sequencing

    22q13.3 interstitial microdeletion detected by array-CGH analysis. A, aligned aCGH profile (P37–38, P43–44: 180k Agilent kit; P42: 244k Agilent kit) details of all interstitial deletions; the deleted regions are shaded. B, map of the distal 22q13.3 region; the deletions are represented by black bars; the region overlapping the SHANK3 gene is shaded in light blue. All genes mapping in the region are shown. C, sequence alignment of the breakpoint junctions of subject P42 showing the homology with three genomic regions. The proximal breakpoint sequence is shown in red, the middle 24 bases in inverted orientation are blue, the distal breakpoint sequence in green; microhomologies between sequences at the breakpoints are depicted in bold. D, cartoon showing the respective position and orientation of the breakpoint sequences in P42 as arrows, colored as in C.

    Journal: PLoS Genetics

    Article Title: Molecular Mechanisms Generating and Stabilizing Terminal 22q13 Deletions in 44 Subjects with Phelan/McDermid Syndrome

    doi: 10.1371/journal.pgen.1002173

    Figure Lengend Snippet: 22q13.3 interstitial microdeletion detected by array-CGH analysis. A, aligned aCGH profile (P37–38, P43–44: 180k Agilent kit; P42: 244k Agilent kit) details of all interstitial deletions; the deleted regions are shaded. B, map of the distal 22q13.3 region; the deletions are represented by black bars; the region overlapping the SHANK3 gene is shaded in light blue. All genes mapping in the region are shown. C, sequence alignment of the breakpoint junctions of subject P42 showing the homology with three genomic regions. The proximal breakpoint sequence is shown in red, the middle 24 bases in inverted orientation are blue, the distal breakpoint sequence in green; microhomologies between sequences at the breakpoints are depicted in bold. D, cartoon showing the respective position and orientation of the breakpoint sequences in P42 as arrows, colored as in C.

    Article Snippet: C, details of the of array-CGH analysis using an oligonucleotide-based 22q13 custom array (eArray, Agilent) showing the breakpoint regions on chromosome 22q (left) and 12q (right) in cases P15/P16.

    Techniques: Sequencing

    Molecular karyotyping was performed by array-CGH on the proband’s DNA using an Agilent 44 K array platform with a resolution of approximately 100 kb. Based on the physical mapping positions of the March 2006 Assembly (NCBI36/hg18) of the UCSC Genome Browser, this analysis showed a duplication of approximately 34 Mb that involved the 9p24.3-p13.3 region, with the breakpoint falling between 601,628 bp (first duplicated oligomer) and 34,638,095 bp (last duplicated oligomer).

    Journal: BMC Endocrine Disorders

    Article Title: Long-term auxological and endocrinological evaluation of patients with 9p trisomy: a focus on the growth hormone-insulin-like growth factor-I axis

    doi: 10.1186/1472-6823-14-3

    Figure Lengend Snippet: Molecular karyotyping was performed by array-CGH on the proband’s DNA using an Agilent 44 K array platform with a resolution of approximately 100 kb. Based on the physical mapping positions of the March 2006 Assembly (NCBI36/hg18) of the UCSC Genome Browser, this analysis showed a duplication of approximately 34 Mb that involved the 9p24.3-p13.3 region, with the breakpoint falling between 601,628 bp (first duplicated oligomer) and 34,638,095 bp (last duplicated oligomer).

    Article Snippet: When possible, CGH array analysis was performed using the Agilent Human Genome CGH Microarray Kit 44 K (Agilent Technologies, Santa Clara, California, USA).

    Techniques:

    Array-CGH profiles of MUG-Chor1 phenotypes. Comparative genome hybridization of 100 large cells (red line) and small cells (blue line) each yielded identical chromosomal profiles. Both populations show gains at chromosomes 2q, 5q, 7, 17q and losses at 2q, 6p, 9p, 10p, 10q, 12p, 17p and 22. Small gains at chromosomes 2q as well as a small loss at chromosome 17q were detected in the large cell phenotype. This indicates that both morphologically different cell types evolved from a common clonal origin. Bars on the left of the moving average indicate losses of DNA. Bars on the right of the moving average indicate gains of DNA. Both profiles are in line with previously published data [8] .

    Journal: PLoS ONE

    Article Title: Resolving Tumor Heterogeneity: Genes Involved in Chordoma Cell Development Identified by Low-Template Analysis of Morphologically Distinct Cells

    doi: 10.1371/journal.pone.0087663

    Figure Lengend Snippet: Array-CGH profiles of MUG-Chor1 phenotypes. Comparative genome hybridization of 100 large cells (red line) and small cells (blue line) each yielded identical chromosomal profiles. Both populations show gains at chromosomes 2q, 5q, 7, 17q and losses at 2q, 6p, 9p, 10p, 10q, 12p, 17p and 22. Small gains at chromosomes 2q as well as a small loss at chromosome 17q were detected in the large cell phenotype. This indicates that both morphologically different cell types evolved from a common clonal origin. Bars on the left of the moving average indicate losses of DNA. Bars on the right of the moving average indicate gains of DNA. Both profiles are in line with previously published data [8] .

    Article Snippet: Array-CGH Array-CGH analysis of MUG-Chor1 samples was performed using SurePrint G3 Human CGH Microarrays 8×60K (Agilent Technologies, Santa Clara, USA) with the Bioprime Array CGH Genomic Labeling System (Life Technologies, Carlsbad, USA) according to the manufacturers' manual.

    Techniques: Hybridization

    cDNA microarray-based CGH analysis of chromosome 8q in BRCAx subgroups. Average copy number ratios for group A (yellow) and group B (blue) are shown for clones on chromosome 8q. The position of the clones on chromosome 8 is shown in Mbs from the 8p telomere, as given by alignment to the draft human genome sequence (see Materials and Methods ). Seventeen clones on 8q24 that were found to be different (α

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Molecular classification of familial non-BRCA1/BRCA2 breast cancer

    doi: 10.1073/pnas.0533805100

    Figure Lengend Snippet: cDNA microarray-based CGH analysis of chromosome 8q in BRCAx subgroups. Average copy number ratios for group A (yellow) and group B (blue) are shown for clones on chromosome 8q. The position of the clones on chromosome 8 is shown in Mbs from the 8p telomere, as given by alignment to the draft human genome sequence (see Materials and Methods ). Seventeen clones on 8q24 that were found to be different (α

    Article Snippet: cDNA microarrays used for CGH analysis were constructed at Agilent Technologies (Palo Alto, CA), and contained 11,367 cDNA clones (representing ≈8,700 unique known genes and 2,000 ESTs) from the previously mentioned collection.

    Techniques: Microarray, Clone Assay, Sequencing

    Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , Microarray CGH profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .

    Journal: Nature

    Article Title: Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

    doi: 10.1038/nature13833

    Figure Lengend Snippet: Genomic rearrangements and transcriptional dysregulation in rad21-K1 a , Microarray CGH profile of rad21-K1 . Genomic DNA isolated from rad21-K1 and wild type was labeled with cy5-dCTP and cy3-dCTP, respectively. The log2(cy5/cy3 signal ratio) was plotted to detect copy number differences between the two strains. Several copy number gains were identified in rad21-K1 . All changes were flanked by highly homologous sequences. SPAC212.08c and SPAC212.12 share a 372bp DNA stretch that shows 97% sequence similarity. SPAC27D7.09c and SPAC27D7.11c share a 560bp DNA stretch that shows 88% sequence similarity. Pericentromeric heterochromatin contains a specific class of repeat elements, referred to as dg/dh repeats. b , Relative expression values (mutants/wild type) were plotted to detect read-through transcripts in the indicated strains. All pairs of convergent genes were aligned at the 3’ end of the second gene in the pair. Note that rad21-K1 cells show increased levels of read-through transcripts that were further enhanced in a pht1Δ rad21-K1 double mutant lacking the histone variant H2A.Z known to prevent their accumulation 35 .

    Article Snippet: Comparative genomic hybridization CGH analysis was performed using our custom Agilent microarray (4×44K format) .

    Techniques: Microarray, Isolation, Labeling, Sequencing, Expressing, Mutagenesis, Variant Assay

    Y MAP visualization of SNP-CGH data for three T1FH clones. The copy numbers and SNP-allele ratios of all three T1FH samples were visualized with Y MAP ( 49 ). Changes in the copy number estimate for regions relative to the parental strain are illustrated by dark bars drawn up- or downward, depending on the direction and magnitude of the change. These strains appear to be tetraploid on the basis of the copy number estimates for Chr7 (and most of ChrR in clone T1FHb), which are 3/4 of the other chromosomes. Color illustrates SNP status across regions. Heterozygous regions are gray, white regions do not have SNPs in the SC5314 reference sequence, and cyan is homozygous “a” alleles (e.g., aaaa on Chr5 in all three clones and ChrR in T1FHa and T1FHc and aaa in T1FHb). Intermediate ratios are indicated by intermediate colors. Blue shade represents more copies of “a” alleles (e.g., aab on the central trisomic region of ChrR in T1FHb), and purple shade represents more copies of the “b” alleles (e.g., abb on Chr7 in all three clones). The portion of ChrR in clone T1FHb to the right of the rDNA region (blue dot) is present in five copies. Major repeat sequences are represented by black dots.

    Journal: mSphere

    Article Title: Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans

    doi: 10.1128/mSphere.00167-17

    Figure Lengend Snippet: Y MAP visualization of SNP-CGH data for three T1FH clones. The copy numbers and SNP-allele ratios of all three T1FH samples were visualized with Y MAP ( 49 ). Changes in the copy number estimate for regions relative to the parental strain are illustrated by dark bars drawn up- or downward, depending on the direction and magnitude of the change. These strains appear to be tetraploid on the basis of the copy number estimates for Chr7 (and most of ChrR in clone T1FHb), which are 3/4 of the other chromosomes. Color illustrates SNP status across regions. Heterozygous regions are gray, white regions do not have SNPs in the SC5314 reference sequence, and cyan is homozygous “a” alleles (e.g., aaaa on Chr5 in all three clones and ChrR in T1FHa and T1FHc and aaa in T1FHb). Intermediate ratios are indicated by intermediate colors. Blue shade represents more copies of “a” alleles (e.g., aab on the central trisomic region of ChrR in T1FHb), and purple shade represents more copies of the “b” alleles (e.g., abb on Chr7 in all three clones). The portion of ChrR in clone T1FHb to the right of the rDNA region (blue dot) is present in five copies. Major repeat sequences are represented by black dots.

    Article Snippet: SNP-CGH array analysis was performed with custom Agilent arrays (eArray Design ID 038464 [ ]).

    Techniques: Clone Assay, Sequencing

    Representative TCR rearrangements in ALCL as detected by Gene Scan PCR and CGH. ( a ) During normal T cell development, rearrangement of TCR genes occurs in a temporal manner whereby rearrangement of δ precedes γ, which is followed by β and then α, the latter of which coincides with deletion of the δ locus. DP, double positive; ISP, intermediate single positive; SP, single positive. ( b ) Typical PCR from DNA (γ, β, δ) or RNA (α) depicting the presence/absence and type of clonal rearrangements for each of the four TCR categories identified are shown, as are Agilent 180K CGH TCRα/δ profiles. ( c ) Three examples representing the range of CGH TCRβ V-J rearrangements observed among the TCRαβ cases: absent (12 out of 17), oligoclonal (2 out of 17) or clonal (3 out of 17). ( d ) The percentage of human ALCL categorized as having either TCR germ line (GL), TCRαβ (TCR AB), TCRγδ (TCR GD) or TCRγ only (TCR G) rearrangements. ND, not determined.

    Journal: Nature Communications

    Article Title: Anaplastic large cell lymphoma arises in thymocytes and requires transient TCR expression for thymic egress

    doi: 10.1038/ncomms10087

    Figure Lengend Snippet: Representative TCR rearrangements in ALCL as detected by Gene Scan PCR and CGH. ( a ) During normal T cell development, rearrangement of TCR genes occurs in a temporal manner whereby rearrangement of δ precedes γ, which is followed by β and then α, the latter of which coincides with deletion of the δ locus. DP, double positive; ISP, intermediate single positive; SP, single positive. ( b ) Typical PCR from DNA (γ, β, δ) or RNA (α) depicting the presence/absence and type of clonal rearrangements for each of the four TCR categories identified are shown, as are Agilent 180K CGH TCRα/δ profiles. ( c ) Three examples representing the range of CGH TCRβ V-J rearrangements observed among the TCRαβ cases: absent (12 out of 17), oligoclonal (2 out of 17) or clonal (3 out of 17). ( d ) The percentage of human ALCL categorized as having either TCR germ line (GL), TCRαβ (TCR AB), TCRγδ (TCR GD) or TCRγ only (TCR G) rearrangements. ND, not determined.

    Article Snippet: To refine the TCR status, 180K Agilent CGH array analysis and PCR detection of clonal TCRα transcripts from complementary DNA (cDNA) using Vα and Cα primers, was performed for selected cases ( ).

    Techniques: Polymerase Chain Reaction

    a Overview of 1 Mb at 20q13.13 chromosome region with five reported overlapping deletions in medical literature: Decipher309, Decipher265392, Decipher257542, Decipher258702, Patient01975-5515, and index-patient. Gray shadow highlights the smallest region of overlap (SRO); the proband carried the smallest 63 kb deletion at 20q13.13 chromosome region harboring two genes ADNP and DPM1 . The ADNP gene in Helsmoortel–van der Aa syndrome is highlighted in yellow. b 60K array-CGH showed a 63 kb interstitial deletion at chromosome 20q13.13 containing ADNP and DPM1 . c Quantitative real-time PCR showed that the deletion occurred de novo in the proband with primers in exons 1 and 5 of ADNP gene (index-patient: purple color; mother: pink color; father: blue color; pool of male control: light blue color; pool of female control: yellow color)

    Journal: European Journal of Human Genetics

    Article Title: A heterozygous microdeletion of 20q13.13 encompassing ADNP gene in a child with Helsmoortel–van der Aa syndrome

    doi: 10.1038/s41431-018-0165-8

    Figure Lengend Snippet: a Overview of 1 Mb at 20q13.13 chromosome region with five reported overlapping deletions in medical literature: Decipher309, Decipher265392, Decipher257542, Decipher258702, Patient01975-5515, and index-patient. Gray shadow highlights the smallest region of overlap (SRO); the proband carried the smallest 63 kb deletion at 20q13.13 chromosome region harboring two genes ADNP and DPM1 . The ADNP gene in Helsmoortel–van der Aa syndrome is highlighted in yellow. b 60K array-CGH showed a 63 kb interstitial deletion at chromosome 20q13.13 containing ADNP and DPM1 . c Quantitative real-time PCR showed that the deletion occurred de novo in the proband with primers in exons 1 and 5 of ADNP gene (index-patient: purple color; mother: pink color; father: blue color; pool of male control: light blue color; pool of female control: yellow color)

    Article Snippet: Agilent 60K array-CGH analysis showed a heterozygous interstitial deletion at 20q13.13 chromosome with three probes (A_16_P03530666, A_14_P134776, and A_14_P104282), log2 ratio = −0.85, encompassing two genes: ADNP and DPM1 , chr20:g.(49,457,856_49,508,676)_(49,571,808_49,620,163)del (hg19, ) ( ) (Fig. ).

    Techniques: Real-time Polymerase Chain Reaction