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acgh g3 human 1×1m array  (Agilent technologies)


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    Structured Review

    Agilent technologies acgh g3 human 1×1m array
    Acgh G3 Human 1×1m Array, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/1m+acgh+array/pmc04562980-112-4-3
    Average 90 stars, based on 1 article reviews
    acgh g3 human 1×1m array - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Isolation:

    Article Title: A de novo 13q31.3 microduplication encompassing the miR-17 ~ 92 cluster results in features mirroring those associated with Feingold syndrome 2.
    Article Snippet: Hemizygosity of the MIR17HG gene encoding the miR-17 ~ 92 cluster is associated with Feingold syndrome 2 characterized by intellectual disability, skeletal abnormalities, short stature, and microcephaly.. Here, we report on a female with a de novo 13q31.3 microduplication encompassing MIR17HG but excluding GPC5.. She presented developmental delay, skeletal and digital abnormalities, and features such as tall stature and macrocephaly mirroring those of Feingold syndrome 2 patients.

    DNA Extraction:

    Article Title: A de novo 13q31.3 microduplication encompassing the miR-17 ~ 92 cluster results in features mirroring those associated with Feingold syndrome 2.
    Article Snippet: Hemizygosity of the MIR17HG gene encoding the miR-17 ~ 92 cluster is associated with Feingold syndrome 2 characterized by intellectual disability, skeletal abnormalities, short stature, and microcephaly.. Here, we report on a female with a de novo 13q31.3 microduplication encompassing MIR17HG but excluding GPC5.. She presented developmental delay, skeletal and digital abnormalities, and features such as tall stature and macrocephaly mirroring those of Feingold syndrome 2 patients.

    Generated:

    Article Title: MAID : An effect size based model for microarray data integration across laboratories and platforms
    Article Snippet: These datasets were collected using two different versions of Agilent array technology. .. One dataset was generated using two-channel Agilent Human 1 cDNA array platform containing 12,814 probes. ..

    Microarray:

    Article Title: Meta-Analysis of Gene Expressions in Testicular Germ Cell Tumor Histologies
    Article Snippet: .. The second microarray [ ] used Agilent Human 1 A oligo assay (Agilent Technologies Inc, Palo Alto, CA, USA) to analyze RNA expression and was available in GEO at ascension number GSE 1818 ( http:ww.ncbi.gov.gen/query/ace.cgi?acc.GSE 1818) and included three samples of NT, three samples of GCNIS, three samples of SE, five samples of EC, four samples of YST, four samples of YST, and one sample of CC. ..

    Article Title: Advanced analysis and visualization of gene copy number and expression data
    Article Snippet: .. The CGH experiments were performed with cDNA arrays on Human 1 cDNA microarray slides (Agilent Technologies, Palo Alto, CA, USA). ..

    Article Title: CGHpower: exploring sample size calculations for chromosomal copy number experiments
    Article Snippet: .. They will be referred to as Chin et al. [ ], Douglas et al. [ ], Fridlyand et al. [ ], Myllykangas et al. [ ], Nymark et al. [ ], Postma et al. [ ], Smeets et al. [ ] and Wrage et al. [ ] A total of five different array types were used among the data sets: VUmc 30 K spotted oligo [ ] for data sets [ , , ], Agilent Human 1 cDNA Microarray for [ , ], 3 K BAC array [ ] for [ ], 2 K BAC array [ ] for [ ] and 6 K BAC array for [ ]. ..

    Article Title: Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    Article Snippet: .. In a recent study, we compared several Affymetrix platforms (for which probe sequence information was available) to the Agilent Human 1 cDNA microarray platform [ ]. .. Probe sequence information was unavailable for the Agilent platform except for a 100 base lead sequence at one end of each cDNA probe.

    Article Title: Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer
    Article Snippet: .. Copy number variation data for primary ovarian tumors was downloaded from TCGA ( http://tcga.cancer.gov/ ) and CBS data files from the Agilent SurePrint G3 Human 1 M CGH (Comparative Genomic Hybridization) Microarray with the label mskcc.org_OV.CGH-1×1M_G4447A were analyzed. ..

    RNA Expression:

    Article Title: Meta-Analysis of Gene Expressions in Testicular Germ Cell Tumor Histologies
    Article Snippet: .. The second microarray [ ] used Agilent Human 1 A oligo assay (Agilent Technologies Inc, Palo Alto, CA, USA) to analyze RNA expression and was available in GEO at ascension number GSE 1818 ( http:ww.ncbi.gov.gen/query/ace.cgi?acc.GSE 1818) and included three samples of NT, three samples of GCNIS, three samples of SE, five samples of EC, four samples of YST, four samples of YST, and one sample of CC. ..

    Labeling:

    Article Title: Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation
    Article Snippet: .. Briefly, 20 μg of total RNA were direct-labeled with Cy-3 and Cy-5, and labeled cDNAs were hybridized overnight to Agilent Human 1 cDNA arrays (G4100a, Agilent Technologies, Palo Alto, CA) containing 16,142 features representing approximately 10,500 unique genes. .. After washing, the microarrays were scanned in an Agilent model G2505A microarray scanner.

    BAC Assay:

    Article Title: CGHpower: exploring sample size calculations for chromosomal copy number experiments
    Article Snippet: .. They will be referred to as Chin et al. [ ], Douglas et al. [ ], Fridlyand et al. [ ], Myllykangas et al. [ ], Nymark et al. [ ], Postma et al. [ ], Smeets et al. [ ] and Wrage et al. [ ] A total of five different array types were used among the data sets: VUmc 30 K spotted oligo [ ] for data sets [ , , ], Agilent Human 1 cDNA Microarray for [ , ], 3 K BAC array [ ] for [ ], 2 K BAC array [ ] for [ ] and 6 K BAC array for [ ]. ..

    Sequencing:

    Article Title: Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    Article Snippet: .. In a recent study, we compared several Affymetrix platforms (for which probe sequence information was available) to the Agilent Human 1 cDNA microarray platform [ ]. .. Probe sequence information was unavailable for the Agilent platform except for a 100 base lead sequence at one end of each cDNA probe.

    Hybridization:

    Article Title: Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer
    Article Snippet: .. Copy number variation data for primary ovarian tumors was downloaded from TCGA ( http://tcga.cancer.gov/ ) and CBS data files from the Agilent SurePrint G3 Human 1 M CGH (Comparative Genomic Hybridization) Microarray with the label mskcc.org_OV.CGH-1×1M_G4447A were analyzed. ..



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    Agilent technologies acgh arrays (244k or 1m platform
    Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. (a) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. (b) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent <t>aCGH</t> arrays <t>(244K</t> or 1M platform as shown) indicates highly altered profiles. Samples are sorted according to their chromosome 10q23 (encoding PTEN) copy-number status (heatmap; red indicates gain/amplification, blue indicates loss/deletion on scale shown at bottom; white is copy-number neutral). Chromosomes are indicated at left and are scaled genomically. Highlighted at right are focal amplifications of the 3p14.1 locus encoding MITF (top) and focal deletions affecting 9p21.3 encoding CDKN2A and CDKN2B (bottom). (c) Statistically significant genomic aberrations (red is amplification, blue is deletion) for the panel of 31 melanoma cell lines are shown (assessed by RAE; plotted are regions with FDR≤15%, autosomes indicated at center in genomic coordinates, centromeres in red, acrocentric arms in black).
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    Image Search Results


    Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. (a) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. (b) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent aCGH arrays (244K or 1M platform as shown) indicates highly altered profiles. Samples are sorted according to their chromosome 10q23 (encoding PTEN) copy-number status (heatmap; red indicates gain/amplification, blue indicates loss/deletion on scale shown at bottom; white is copy-number neutral). Chromosomes are indicated at left and are scaled genomically. Highlighted at right are focal amplifications of the 3p14.1 locus encoding MITF (top) and focal deletions affecting 9p21.3 encoding CDKN2A and CDKN2B (bottom). (c) Statistically significant genomic aberrations (red is amplification, blue is deletion) for the panel of 31 melanoma cell lines are shown (assessed by RAE; plotted are regions with FDR≤15%, autosomes indicated at center in genomic coordinates, centromeres in red, acrocentric arms in black).

    Journal: Oncogene

    Article Title: Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring V600E BRAF

    doi: 10.1038/onc.2011.250

    Figure Lengend Snippet: Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. (a) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. (b) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent aCGH arrays (244K or 1M platform as shown) indicates highly altered profiles. Samples are sorted according to their chromosome 10q23 (encoding PTEN) copy-number status (heatmap; red indicates gain/amplification, blue indicates loss/deletion on scale shown at bottom; white is copy-number neutral). Chromosomes are indicated at left and are scaled genomically. Highlighted at right are focal amplifications of the 3p14.1 locus encoding MITF (top) and focal deletions affecting 9p21.3 encoding CDKN2A and CDKN2B (bottom). (c) Statistically significant genomic aberrations (red is amplification, blue is deletion) for the panel of 31 melanoma cell lines are shown (assessed by RAE; plotted are regions with FDR≤15%, autosomes indicated at center in genomic coordinates, centromeres in red, acrocentric arms in black).

    Article Snippet: All mutations were confirmed by sequencing with an orthogonal platform ( Supplementary Figure 1 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 1 caption a7 Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. ( a ) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. ( b ) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent aCGH arrays (244K or 1M platform as shown) indicates highly altered profiles.

    Techniques: Mutagenesis, Amplification

    Characterization of PTEN status of V600EBRAF-mutant melanoma cell lines. (a) Nine V600EBRAF cell lines that expressed minimal to no PTEN protein and high levels of phosphorylated AKT (ser473 and thr308) were identified by immunoblot. Two of the nine V600EBRAF, PTEN-null cell lines, SKMEL-207 and A2058, were also RB1 null. (b) PTEN mRNA expression was detected by reverse transcription–PCR in six of the nine PTEN-null models. SKMEL-207 expresses a low level of PTEN mRNA. (c) Array CGH-based determination of DNA copy-number alterations identifies frequent single copy loss (light blue) of 10q encompassing PTEN with less common focal homozygous deletions (dark blue) with diverse breakpoints affecting the gene in the four cell lines indicated. (d) Probe level and segmentation data in SKMEL-178 from both Agilent 244K- and 1M-feature arrays (gray and blue/red, respectively). The higher resolution 1M platform (blue dots/red line) robustly identified a focal and intragenic micro-scale deletion encompassing exon 2 of PTEN that was not detected by the lower-resolution array.

    Journal: Oncogene

    Article Title: Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring V600E BRAF

    doi: 10.1038/onc.2011.250

    Figure Lengend Snippet: Characterization of PTEN status of V600EBRAF-mutant melanoma cell lines. (a) Nine V600EBRAF cell lines that expressed minimal to no PTEN protein and high levels of phosphorylated AKT (ser473 and thr308) were identified by immunoblot. Two of the nine V600EBRAF, PTEN-null cell lines, SKMEL-207 and A2058, were also RB1 null. (b) PTEN mRNA expression was detected by reverse transcription–PCR in six of the nine PTEN-null models. SKMEL-207 expresses a low level of PTEN mRNA. (c) Array CGH-based determination of DNA copy-number alterations identifies frequent single copy loss (light blue) of 10q encompassing PTEN with less common focal homozygous deletions (dark blue) with diverse breakpoints affecting the gene in the four cell lines indicated. (d) Probe level and segmentation data in SKMEL-178 from both Agilent 244K- and 1M-feature arrays (gray and blue/red, respectively). The higher resolution 1M platform (blue dots/red line) robustly identified a focal and intragenic micro-scale deletion encompassing exon 2 of PTEN that was not detected by the lower-resolution array.

    Article Snippet: All mutations were confirmed by sequencing with an orthogonal platform ( Supplementary Figure 1 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 1 caption a7 Landscape of copy-number alterations in V600EBRAF-mutant melanoma cell lines. ( a ) A total of 149 melanoma cell lines were characterized for mutations in BRAF and NRAS using mass spectrometric genotyping. ( b ) Segmented DNA copy-number data for 31 V600EBRAF cell lines characterized on one of two Agilent aCGH arrays (244K or 1M platform as shown) indicates highly altered profiles.

    Techniques: Mutagenesis, Western Blot, Expressing