Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA143261 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE17342: The role of miRNA in Wilms' tumorigenesis GSE28397: Copy number alteration in Wilms' tumor with custom-designed miRNA probes GSE28400: MIR-204 target gene Refer to individual Series
2012-03-30 | E-GEOD-28401 | biostudies-arrayexpress
Project description:Genome-wide DNA copy number was studied to determine whether the Wilms' tumor samples generally show normal copy number variation comparing to the colon tumor samples We used custom Nimblegen microarrays to determine the genome-wide DNA copy number in human Wilms' Tumor samples We isolated genomic DNA from human Wilms' tumor tissues and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).
2011-08-28 | E-GEOD-29374 | biostudies-arrayexpress
Project description:The aim of this study is to discover loss of specific miRNA loci in Wilms' tumors using array CGH. Custom arrays were designed based on the Agilent 2x105K Human Whole Genome Genomic microarray with Agilent’s eArray program (https://earray.chem.agilent.com/earray/), with additional probes that cover all miRNA regions (200 bps before, within and after each miRNA from miRBase v13, with each probe in triplicates to enhance the reliability). All custom-designed probes were designed in UCSC hg18. Probes from Agilent’s database were lifted-over from hg19 to hg18 (LiftOver tool: http://genome.ucsc.edu).
2012-03-31 | GSE28397 | GEO
Project description:Genome-wide DNA copy number was studied to determine whether the Wilms' tumor samples generally show normal copy number variation comparing to the colon tumor samples We used custom Nimblegen microarrays to determine the genome-wide DNA copy number in human Wilms' Tumor samples
2011-08-29 | GSE29374 | GEO
Project description:The aim of this study is to discover loss of specific miRNA loci in Wilms' tumors using array CGH. Custom arrays were designed based on the Agilent 2x105K Human Whole Genome Genomic microarray with Agilent’s eArray program (https://earray.chem.agilent.com/earray/), with additional probes that cover all miRNA regions (200 bps before, within and after each miRNA from miRBase v13, with each probe in triplicates to enhance the reliability). All custom-designed probes were designed in UCSC hg18. Probes from Agilent’s database were lifted-over from hg19 to hg18 (LiftOver tool: http://genome.ucsc.edu). The Agilent 2x105K custom-design whole genome microarray was used to analyze genomic alterations in Wilms' tumor samples compared to normal human genomic DNA (Promega p/n G1523).
2012-03-30 | E-GEOD-28397 | biostudies-arrayexpress
Project description:DNA copy number variation from human Wilms' Tumor samples
| PRJNA140217 | ENA
Project description:In order to examine if acquired copy number alterations in DNA repair genes is commonly observed in therapy-related AML, we used this custom built NimbleGen array with dense tiling of probes in 170 DNA repair genes to interrogate paired normal (skin) and tumor (bone marrow) samples.
2013-12-13 | GSE53250 | GEO
Project description:Copy number variations and genomic rearrangements in the CFH-CFHRs region were assessed with a custom-designed high-density 8x15k oligonucleotide CGH arrays spanning the RCA gene cluster region in human chromosome 1q32 (median resolution of 110 bp) (AMADID 040193, Agilent Technologies, Santa Clara, CA). A healthy male donor sample, fully genotyped for that region, was used as hybridization control. Microarray data were extracted and visualized using the Feature Extraction Software v10.7 and Genomic Workbench Standard Edition 7.0 (Agilent Corp, Santa Clara, CA). Copy number altered regions were detected using ADM-2 (set as 5) statistic provided by DNA Analytics, with a minimum number of 5 consecutive probes. Genomic build hg19 was used for the experiment.
2013-05-28 | GSE45585 | GEO
Project description:Abstract: Background: MiRNA signatures in human sera have been reported for various tumor diseases. Here we generated miRNA profiles analyzing 1205 mature miRNA transcripts of serum samples of Wilms tumor patients, taken prior and after chemotherapy according to SIOP protocol 2001. Using a feature subset selection filter approach we identified a minimal number of miRNAs with a maximum contribution for the classification between treated and untreated patients and between patients and controls. Results: Analyzing 1205 mature miRNAs, we separated controls and Wilms tumor patients prior chemotherapy with an accuracy of 0.81. We obtained a similar accuracy (0.82) for the separation between controls and sera of Wilms tumor patients after preoperative chemotherapy. We identified 23 miRNAs that were differentially expressed in both comparisons. Subset selection improved the overall classification accuracy between controls and Wilms tumor patients prior and after chemotherapy to 0.94 and 0.91, respectively. Subset selection also allowed separating between Wilms tumor patients prior and after chemotherapy with an accuracy of 0.98. Conclusion: Our analysis identified serum based miRNA signatures that allowed separating between controls, untreated Wilms tumor patients, and Wilms tumor patients after chemotherapy with high accuracy for each of these comparisons.
2014-12-31 | GSE48137 | GEO
Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0).
2013-08-09 | GSE41488 | GEO