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Expression data from primary breast tumors (NUH)

ABSTRACT: Frozen tissue specimens from primary breast tumors were collected under approved protocols and profiled using Affymetrix U133 series expression microarrays. This cohort was assembled at the National University Hospital (NUH), Singapore in 2003, and profiled at the Genome Institute of Singapore, Microarray and Expression Genomics Lab. Dr. Lance D. Miller (Wake Forest University School of medicine) directed the profiling work. A publication describing the generation of these data is not yet available. However, these data can be used alongside other Affymetrix breast tumour data sets to form large meta-cohorts for breast cancer research, as was done in Lasham et. al. J Natl Cancer Inst. 2012 Jan 18;104(2):133-146.

ORGANISM(S): Homo sapiens

PROVIDER: GSE36772 | GEO | 2012/03/31

SECONDARY ACCESSION(S): PRJNA156849

REPOSITORIES: GEO

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Expression data from primary breast tumors (NUH)

Project description:Frozen tissue specimens from primary breast tumors were collected under approved protocols and profiled using Affymetrix U133 series expression microarrays. This cohort was assembled at the National University Hospital (NUH), Singapore in 2003, and profiled at the Genome Institute of Singapore, Microarray and Expression Genomics Lab. Dr. Lance D. Miller (Wake Forest University School of medicine) directed the profiling work. A publication describing the generation of these data is not yet available. However, these data can be used alongside other Affymetrix breast tumour data sets to form large meta-cohorts for breast cancer research, as was done in Lasham et. al. J Natl Cancer Inst. 2012 Jan 18;104(2):133-146. Frozen tumor tissues comprising of >60% tumor cellularity were extracted for total RNA and hybridized on Affymetrix microarrays. Clinical data was requested, but not provided by submitter

2012-03-30 | E-GEOD-36772 | biostudies-arrayexpress

Expression data from primary breast tumors (Auckland)

Project description:Frozen tissue specimens from primary breast tumors were collected and profiled using Affymetrix U133 plus 2 expression microarrays. A publication describing the generation of these data is not yet available. However, these data can be used alongside other Affymetrix breast tumour data sets to form large meta-cohorts for breast cancer research, as was done in Lasham et. al. J Natl Cancer Inst. 2012 Jan 18;104(2):133-146.

2012-03-31 | GSE36771 | GEO

Expression data from primary breast tumors (IJB+OXF)

Project description:Frozen tissue specimens from primary breast tumors were collected under IRB-approved protocols from 2 medical centers and profiled using Affymetrix U133 series expression microarrays. This cohort comprises of two subcohorts derived from the Institute Jules Bordet (IJB), Brussels (n=41) (2002) and Guys Hospital, London (n=7) (2003). Dr. Christos Sotiriou (Institute Jules Bordet) directed the microarray work in Brussels. A publication describing the generation of these data is not yet available. However, these data can be used alongside other Affymetrix breast tumour data sets to form large meta-cohorts for breast cancer research, as was done in Lasham et. al. J Natl Cancer Inst. 2012 Jan 18;104(2):133-146.

2012-03-31 | GSE36773 | GEO

Expression data from primary breast tumors (Auckland)

2012-03-30 | E-GEOD-36771 | biostudies-arrayexpress

Expression data from primary breast tumors (IJB+OXF)

2012-03-30 | E-GEOD-36773 | biostudies-arrayexpress

Single Cell RNA Profiles of a Human Triple Negative Breast Cancer

Project description:To investigate the transcriptional dynamics of the breast tumor microenvironment, remnant surgical tissue from an AJCC stage III triple negative invasive ductal carcinoma resected at Wake Forest Baptist Medical Center (WFBMC) in Winston Salem, NC, was accessed via Wake Forest University Health Sciences Institutional Review Board protocol IRB00048977 and expression profiled by single cell RNA sequencing. Approximately 770 high-quality cell expression profiles were identified.

2021-11-13 | GSE188600 | GEO

Prinary breast cancers and brain metastasis

Project description:Sixteen paired matched samples from primary breast cancers and brain metastases diagnosed between April 1, 2001 and December 31, 2012 were collected from 8 institutions. Brain metastases were identified based on magnetic resonance imaging and/or computed tomography findings. The clinical characteristics of all the patients were obtained from their medical records. This study was approved by the institutional review board of each participating institute (Tokai University School of Medicine; National Hospital Organization Osaka National Hospital; Kinki University School of Medicine; Niigata Cancer Center Hospital; Shizuoka General Hospital; Hokkaido Cancer Center; National Hospital Organization, Tokyo Medical Center; and Gunma Prefectural Cancer Center). Matching primary breast cancers and brain metastases Formalin-Fixed Paraffin-Embedded (FFPE) specimens for gene expression analysis were collected into RNA. RNA from specimens was isolated, and quantity and quality of the each RNA was using an Agilent 2100 Bioanalyzer (Agilent Technologies). Genome-wide expression levels of transcripts were analyzed using the Affymetrix U133A gene chips (Affymetrix) according to the manufacture’s instructions.

2019-09-25 | GSE125989 | GEO

Transcription profiling of human amniotic fluid-derived stem cells (AFSC) treated with ethanol

Project description:The effects of ethanol may vary from induction of apoptosis to the inhibition of proliferation, differentiation, migration or other function. The complex and diverse response of fetal cells to ethanol has prompted us to use a bioinformatics approach to study the effect of ethanol on fetal stem cells derived from the amniotic fluid-derived (AFSC). To characterize the global response of human AFSC to ethanol, gene expression profiles of AFSC treated with or without 100mM ethanol for 48 hours were analyzed. Experiment Overall Design: Two microarrays were performed (AFSC sealed with parafilm for 48 hours treated with or without 100 mM of ethanol). Total RNA was isolated using RNA Bee according to manufacturer's instructions. Fragmented antisense cRNA was used for hybridizing with human U133 A arrays (Affymetrix, Inc. Santa Clara, CA, USA) at the Core Genomic Facility of Wake Forest University School of Medicine. Raw CEL files were provided by the Microarray Core Facility of the Wake Forest University School of Medicine and were then analyzed with a software package AffylmGUI (Affymetrix LIMMA, Linear Models for Microarray Data, Graphical User Interfaces). AffylmGUI reads the raw Affymetrix CEL files directly, summarizes the gene expression values using RMA, and then uses LIMMA to identify statistically significant differences in gene expression. LIMMA fits a linear model for every gene (like ANOVA or multiple regression analysis), and adjusts P values for multiple testings. Differentially expressed genes were identified with a fold change > 1.8.

2009-10-11 | E-GEOD-13569 | biostudies-arrayexpress

A Modular Analysis of Breast Cancer Reveals a Novel Low-Grade Molecular Signature in Estrogen Receptor-Positive Tumors

Project description:Primary human breast tumors were obtained from the National Cancer Centre of Singapore (NCC) Tissue Repository, after appropriate approvals from the NCC Repository and Ethics Committees. Profiled samples contained at least 50% tumor content. Keywords = Gene expression Keywords = Breast Cancer Keywords: other

2006-02-18 | GSE2294 | GEO

Expression Profiles of Breast Tumors from Singapore and Europe

Project description:To facilitate a better understanding of the molecular heterogeneity of breast cancer and to uncover gene-survival associations that segregate with distinct molecular subtypes, we recently compiled a meta-analytical database of over 2,000 human breast tumor expression profiles variously annotated for clinical and pathological variables and derived from various institutions worldwide. This database was utilized for the breast tumor study cited below: Nagalla, et. al., Genome Biology, 2013. While the majority of the tumor expression profiles included in this database derived from publicly accessible microarray repositories, a number of the samples had not been previously published. Here, we describe the origin of these samples and provide their associated clinical and pathological annotations with the hope that other investigators will be able to utilize these data in their own research. Breast tumor samples derived from the Institut Jules Bordet (IJB; Belgium), John Radcliffe Hospital (JRH; Oxford) and the National University Hospital (NUH, Singapore) were profiled on the Affymetrix U133A platform. The number of tumors profiled (n) and the corresponding dates of tumor diagnosis are as follows. IJB: n=41, 1994-2001; JRH: n=8, 1990-1993; and NUH: n=100, 2000-2002.

2013-03-21 | E-GEOD-45255 | biostudies-arrayexpress

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