Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling, comparative genomic hybridization, genotyping and methylation profiling by array of human breast cancer cell lines

ABSTRACT: Integrative analysis of breast cancer cell lines, using expression, comparative genomics, SNP and methylation profiling

ORGANISM(S): Homo sapiens

DISEASE(S): normal

SUBMITTER: Anita Grigoriadis

PROVIDER: E-TABM-928 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparative genomic hybridization of 17 favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome

Project description:We have carried out microarray-based comparative genomic hybridisation (arrayCGH) on 17 Favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome. Tumour DNA was co-hybridised with normal female genomic DNA onto microarrays consisting of 2118 BAC clones with tiling-path coverage of chromosome 1. Data was normalised and quality-filtered, an adapted weights smoothing algorithm fitted, and changes in DNA copy number assessed for each clone.

2006-05-11 | E-TABM-13 | biostudies-arrayexpress

Comparative genomic hybridization of 100 favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome

Project description:We have carried out microarray-based comparative genomic hybridisation (arrayCGH) on 100 favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome. Tumour DNA was co-hybridised with normal female genomic DNA onto microarrays consisting of 4263 BAC clones with an approximate 1Mb spacing throughout the genome. Data was normalised and quality-filtered, an adapted weights smoothing algorithm fitted, and changes in DNA copy number assessed for each clone.

2006-05-11 | E-TABM-10 | biostudies-arrayexpress

Comparative genomic hybridization of human perilobar nephrogenic rest and matching Wilms tumours to identify changes in DNA copy number associated with IGF-driven Wilms tumorigenesis

Project description:We have carried out microarray-based comparative genomic hybridisation (arrayCGH) on 50 perilobar nephrogenic rest and 25 matching Wilms tumours in order to identify changes in DNA copy number associated with IGF-driven Wilms tumorigenesis. All patient samples were formalin fixed-paraffin embedded archival material. Tumour DNA was co-hybridised with normal female genomic DNA onto 5.8K, 0.9Mb-spaced (E-MEXP-213) and/or a 16K, 100kb-spaced BAC array. Data was normalised and quality-filtered, an adapted weights smoothing algorithm fitted, and changes in DNA copy number assessed for each clone.

2009-02-25 | E-TABM-436 | biostudies-arrayexpress

Comparative genomic hybridization of high grade gliomas arising in children and young people

Project description:As genome-scale technologies begin to unravel the complexity of the equivalent tumours in adults, detailed characterisation of high grade gliomas in children have until recently been lacking. In order to validate and extend investigations of the differences between paediatric and adult tumours, we carried out copy number profiling by array CGH using a 32K BAC platform on 63 formalin-fixed paraffin-embedded (FFPE) cases of high grade glioma arising in children and young people (<23 yrs).

2010-07-01 | E-TABM-857 | biostudies-arrayexpress

Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [RNA-Seq]

Project description:In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays). Human samples consisted of total RNA obtained from MDA-MB-231 human breast carcinoma cell line and isolated from three independent cultures of sub-confluent MDA-MB-231 cell lines in exponential phase of growth. Mouse samples were obtained from NOD scid gamma mice, and normal lung tissue was harvested from three independent age-matched mice.

2012-12-14 | E-GEOD-40890 | biostudies-arrayexpress

Comparative genomic hybridization of human breast cancer cell lines

Project description:AM_BreastCancerCellLineExpressionaCGH

2009-02-03 | E-TABM-593 | biostudies-arrayexpress

MBD3 localization by ChIP-seq

Project description:Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS). Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression. Identification of MBD3 localization in human breast cancer cell lines

2013-10-31 | E-GEOD-44737 | biostudies-arrayexpress

Transcription profiling of human breast cancer biopsies taken before and after patients were treated with aromatase inhibitors

Project description:Molecular response to Aromatase Inhibitor Treatment in Primary Breast Cancer

2007-11-29 | E-TABM-180 | biostudies-arrayexpress

Breast cancer cell line MDA-MB-453 response to DHT

Project description:This SuperSeries is composed of the following subset Series: GSE28305: Effect of 5a-dihydrotestosterone on breast cancer cell line MDA-MB-453 GSE28788: Androgen receptor cistrome in breast cancer cell line MDA-MB-453 with 5a-dihydrotestosterone (DHT) stimulation Refer to individual Series

2011-07-10 | E-GEOD-28789 | biostudies-arrayexpress

Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and their interacting stromal fibroblast cells

Project description:Communication and interaction between carcinoma associated fibroblast (CAF) cells and tumor epithelium cells plays a critical role in cancer initiation and progression. However, a mechanistic understanding of how CAFs communicate with tumor cells to promote their proliferation and invasion is far from complete. In this study, we employed a SILAC labeling based co-culture system coupled with mass spectrometry analysis to identify and quantify the early phospho-signaling transductions induced by the crosstalk between CAFs and tumor cells. We performed three-state SILAC labeling for MDA-MB-231 and 82T. 9 million light labeled 82-L cells were co-cultured with medium labeled MDA-MB-231-M cells for 30 minutes. 9 million heavy labeled 82T-H cells were individually cultured in heavy SILAC media with for 30 minutes. Both individually cultured and co-cultured cells were quickly harvested with 9 M urea lysis buffer and mixed together. Mixed lysates were sonicated, reduced, alkylated and digested by trypsin. Tryptic peptides were desalted using SepPak C18 cartridge and followed by phosphotyrosine peptide enrichment using immunoaffinity purification with pY100 antibody. The enriched phosphopeptides were analyzed using a reverse-phase liquid chromatography system interfaced with an LTQ-Orbitrap Velos mass spectrometer. The Proteome Discoverer (v2.0; Thermo Fisher Scientific) suite was used for quantitation and database searches. The tandem mass spectrometry data were searched using SEQUEST search algorithm against a Human RefSeq database supplemented with frequently observed contaminants. The probability of phosphorylation sites was determined from the PhosphoRS algorithm.

2018-10-26 | PXD003544 | Pride

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