Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA90451 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:BAC CGH array profiling using Phi29-amplified colon mucosa of microdissected samples from APC and MYH mutation carriers.
| PRJNA94147 | ENA
Project description:Seventy blastomeres from fourteen frozen-thawed supernumerary human preimplantation embryos were disassociated and genomic was amplified using Multiple Displacement Amplification. BAC array-CGH was performed on the amplified products.
2012-10-15 | GSE34290 | GEO
Project description:Genomic changes in chromosome 8 are commonly observed in breast cancer cell lines and tumors. Fine mapping of such genomic changes, and evaluation of associated expression changes, are expected to provide reagents for diagnosis, insights into understanding the disease, and open up avenues for novel therapeutic intervention. We made an effort to search for genes on chromosome 8 with altered copy number and expression. A high resolution (0.1Mb) bacterial artificial chromosome (BAC) array of chromosome 8 that can detect single copy changes was developed using Phi29 DNA polymerase amplified BAC DNA. Hybridization of DNA from a breast cancer cell line (SKBR3) with two known amplified regions (8q21 and 8q24) resulted in resolving this region into 6 distinct amplicons, in addition identified 3 deleted regions. The boundaries and the peak of each region were verified by FISH, and the extent of amplification/deletion for each region was validated by qPCR. Using these BAC arrays, CGH was performed with a total of eight breast cancer cell lines, and common regions of genomic amplification/deletion were identified by segmentation analysis. Two consensus regions in 8q24 included a 1.2 Mb region (125.3-126.5 Mb) and a 1.0 Mb region (128.1-129.1 Mb) that were amplified in 7/8 cell lines, and in the 8q21 region there was a smaller 0.88 Mb region (86.62-87.50 Mb) amplified in 4/8 cell lines. A global expression analysis was performed for all these cell lines using a high-density oligonucleotide array to identify the genes whose expression correlated with amplification/deletion. Representative genes from 5 commonly amplified regions (REXO1L1, TMEM55A, TRMT12, MTSS1, EIF2C2, MYC) and 2 deleted regions (DPYSL2, NRG1 and NDRG1) were verified by qPCR and RT-qPCR for genomic and expression changes. Validation by RT-qPCR using RNA from 30 breast tumors showed that the TRMT12 (125.5 Mb) gene were overexpressed in many of the tumors. TRMT12 is homolog of a yeast gene encoding tRNA methyltransferase involved in biosythesis of a modified base in a tRNA. It would be interesting to explore the role of TRMT12 and the RNA processing pathway in tumorigenesis. Keywords: Comparative Genomic Hybridization (CGH), Breast cancer cell lines, Expression, BAC array, Oligo expression array
2007-05-07 | GSE6567 | GEO
Project description:Seventy blastomeres from fourteen frozen-thawed supernumerary human preimplantation embryos were disassociated and genomic was amplified using Multiple Displacement Amplification. BAC array-CGH was performed on the amplified products. BAC array-CGH on single blastomeres amplified by Multiple Displacement Amplification.
2012-10-15 | E-GEOD-34290 | biostudies-arrayexpress
Project description:In this study, we extend array CGH technology by making the accurate detection of segmental aneusomies possible from a single lymphoblast and fibroblast following Phi29 DNA polymerase amplification Keywords: array CGH, aCGH
2006-02-16 | GSE4244 | GEO
Project description:Abstract: Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of fresh-frozen and formalin-fixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens. This SuperSeries is composed of the SubSeries listed below.
2006-03-15 | GSE4467 | GEO
Project description:In this study, we extend array CGH technology by making the accurate detection of chromosomal imbalances possible from a single fibroblast and blastomere following Phi29 DNA polymerase amplification. Keywords: CGH
2006-02-01 | GSE3642 | GEO
Project description:Genomic alterations of 332 malignant lymphoma using BAC array CGH analysis
| PRJNA236336 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE4078: Phi29-based amplification of fresh-frozen and FFPE tumor DNA GSE4079: Genome-Wide Gene Dosage Representation in Phi29-Amplified DNA Abstract: Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of fresh-frozen and formalin-fixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens. Refer to individual Series
2006-03-14 | E-GEOD-4467 | biostudies-arrayexpress
Project description:In this study, we extend array CGH technology by making the accurate detection of chromosomal imbalances possible from a single fibroblast and blastomere following Phi29 DNA polymerase amplification. Firstly, array CGH experiments were performed on four different fibroblast cell lines, derived from patients affected by, respectively, trisomy 13, 18, 21, and monosomy X. For each cell line, three single cells were amplified. Following DNA amplification, all cells showed the expected DNA yields (n=12; 1.87 µg plus:minus 0.39). Sex-mismatch array CGH experiments were conducted on amplified DNA samples obtained from each cell. Sex chromosome ploidy levels, as well as all expected autosomal abnormalities were clearly identified. Secondly, we applied single-cell aneuploidy screening for the detection of chromosomal imbalances in preimplantation embryos. DNA from blastomeres from three 7-8 cell-stage embryos was amplified by ï¦29 DNA polymerase. Following DNA amplification, all cells yielded the expected amount of DNA (n=16; 2.45 µg plus:minus 0.41). Chromosomal aneuploidies were accurately detected using a simple and rapid array CGH protocol.
2010-07-01 | E-GEOD-3642 | biostudies-arrayexpress