Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CGH analysis of adrenocortical tumors

ABSTRACT: Adrenocortical tumors are common; their prevalence may reach up to 5-7% in pathological series. Most of them are benign and hormonally inactive, however, rare hormone-secreting (aldosterone and cortisol) and malignant forms are associated with significant morbidity and mortality. The prognosis of adrenocortical cancer (ACC) is poor with an overall five-year survival below 30 %. In this study, CGH analysis was performed on 4 ACC (adrenocortical carcinoma), 4 IA (hormonally inactive adrenocortical adenoma) and 3 CPA (cortisol producing adrenocortical adenoma) samples. Tissue digestion, labeling, hybridization and data analysis of genomic DNA were performed according to the Agilent Technologies (Santa Clara, CA) protocol version 2.0 for 105 K arrays. As expected, many of the observed aberrations were generally consistent with those of other preciously published data and will provide the basis for determination how genomic diversity impacts biological function and human diseases, such as cancer. In this study, biopsies from adrenocortical tumors (4 ACC, 4 IA and 3 CPA samples) were analysed with CGH. Tissue digestion, labeling, hybridization, and data analysis of genomic DNA were performed according to the Agilent Technologies (Santa Clara, CA) protocol version 2.0 for 105 K arrays. Slides were scanned with Agilent Microarray scanner and data were extracted with Feature Extraction software version 9.5.1.1. DNA Analytics software was used (version 4.0.85, Agilent Technologies, Santa Clara, CA) for data analysis. The starting and ending points of the aberrations were confirmed by the ADM-2 algorithm with 6.0 threshold.

ORGANISM(S): Homo sapiens

SUBMITTER: Katalin KÃ¶vesdi

PROVIDER: E-GEOD-17396 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

CGH analysis of adrenocortical tumors

Project description:Adrenocortical tumors are common; their prevalence may reach up to 5-7% in pathological series. Most of them are benign and hormonally inactive, however, rare hormone-secreting (aldosterone and cortisol) and malignant forms are associated with significant morbidity and mortality. The prognosis of adrenocortical cancer (ACC) is poor with an overall five-year survival below 30 %. In this study, CGH analysis was performed on 4 ACC (adrenocortical carcinoma), 4 IA (hormonally inactive adrenocortical adenoma) and 3 CPA (cortisol producing adrenocortical adenoma) samples. Tissue digestion, labeling, hybridization and data analysis of genomic DNA were performed according to the Agilent Technologies (Santa Clara, CA) protocol version 2.0 for 105 K arrays. As expected, many of the observed aberrations were generally consistent with those of other preciously published data and will provide the basis for determination how genomic diversity impacts biological function and human diseases, such as cancer.

2009-08-06 | GSE17396 | GEO

Mice liver and urine LC-MS data

Project description:Mouse livers were analyzed by lipidomics and urine by metabolomics.An Agilent Ultra-Performance Liquid Chromatography/Electrospray Ion Quadrupole Time-of-Flight-Mass Spectrometer (UPLC-ESI-QTOFMS) (Agilent, Santa Clara, CA) was utilized for lipid and other metabolites proofing in this work.

2023-06-07 | PXD041465 | Pride

Genomic profiling of ten prostate cancer cell lines

2011-02-01 | GSE26447 | GEO

Expression of cyclophilin B is associated with malignant progression and regulation of genes

Project description:Microarray was conducted on Illumina Human Ref-6 Version 2 Expression Chip (Illumina, San Diego, CA). Three independent cultures were used for RNA isolation with RNeasy plus mini kit (Qiagen, Valencia, CA). RNA quality was checked by Agilent Bioanalyzer (Agilent, Santa Clara, CA). An Ambion labeling kit was used for labeling cDNA followed by hybridization to Illumina chips. ChIP scan data was extracted by Illumina Beadstudio and subsequently analyzed using Bioconductor lumi package.

2009-04-03 | GSE15505 | GEO

Modulation of microglia-mediated amyloid-beta clearance with nanoformulated polyphenol through the SIRT1-LDLR pathway

Project description:Light-controlled in situ synthesis of DNA microarrays (Affymetrix GeneChip® Mouse Genome 430 2.0) were performed to determine the altered gene expression. Affymetrix algorithm and multiple analysis comparison software were used for assessing gene expression differences, and mRNAs that increased or decreased in the brains of NP(α-M)-treated mice relative to that in the brains of Blank-NP-treated mice were identified. For the assay, total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions. Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

2018-09-14 | GSE119904 | GEO

Maternal Stress and Genomic Variation

Project description:Custom Affymetrix SNP used to assay 24 mothers for desired variants. Data processed using the Affymetrix SNP Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA).

2017-11-30 | GSE107512 | GEO

Genomic profiling of ten prostate cancer cell lines

Project description:Prostate cancer cell lines grow in full serum under standard conditions were profiled on Agilent-014698 Human Genome CGH Microarray 105A. Digestion, labeling, hybridization and data analysis of genomic DNA were performed according to the Agilent Technologies (Santa Clara, CA) protocol version 6.0 for 105 K arrays. Ten prostate cancer cell lines were included in the profiling, 22RV1, C4-2B, CA-hpv-10, DU145, LAPC4, MDAPCa-2b, NCI660, PC3, VCaP, and WPE1-NB26. All cell lines were grown in accordance with the distributor's instructions. All samples except DU145 were hybridized once on 105k Agilent Human Genome CGH microarrays according to manufacturers instructions. Two replicate hybridizations were done for DU145 cell line. Human Adult Male Normal Genomic DNA (6 normal individuals, Promega, #G1471) was used as a reference in all hybridizations. DNA from cell line samples were labeled with Cy5 and DNA from reference were labeled with Cy3.

2011-02-01 | E-GEOD-26447 | biostudies-arrayexpress

Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (MeDIP)

Project description:The analysis of DNA methylation profiles was performed by methylated DNA immunoprecipitation (MeDIP) using anti-5-methylcytidine antibody (Eurogentec, Seraing, Belgium) followed by the Human 244K Agilent CpG island microarray (Agilent, Santa Clara, CA)

2012-03-31 | GSE35312 | GEO

Combination of ABT-869 with SAHA on AML with FLT3-ITD

Project description:For the microarray experiments, MV4-11 and MOLM-14 cells were treated with DMSO control, ABT-869 3 nM, SAHA 6 uM and combination therapy for 24 hours. Cells were then washed in PBS and high-quality total RNA was extracted RNeasy Midi Kit, according to the manufacturer’s instruction (Qiagen, Valencia, USA). RNA quantity, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA, USA). Gene expression profiling was performed using Affymetric U133plus2.0 gene chip (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol.

2011-05-31 | GSE26114 | GEO

Genomic rearrangements in C3 glomerulopathies

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data