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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of breast cancer tissue in a large population-based cohort of Swedish patients

ABSTRACT: Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996. Material was frozen immediatley on dry ice or in liquid nitrogen and stored in -70Â°C freezers. This series contains expression data for n=159 tumors from which RNA could be collected in sufficient amounts and quality for analysis. Experiment Overall Design: All tumor specimens were assessed on U133 A and B arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Alexander Ploner

PROVIDER: E-GEOD-1456 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts.

Pawitan Yudi Y Bjöhle Judith J Amler Lukas L Borg Anna-Lena AL Egyhazi Suzanne S Hall Per P Han Xia X Holmberg Lars L Huang Fei F Klaar Sigrid S Liu Edison T ET Miller Lance L Nordgren Hans H Ploner Alexander A Sandelin Kerstin K Shaw Peter M PM Smeds Johanna J Skoog Lambert L Wedrén Sara S Bergh Jonas J

Breast cancer research : BCR 20051003 6

<h4>Introduction</h4>Adjuvant breast cancer therapy significantly improves survival, but overtreatment and undertreatment are major problems. Breast cancer expression profiling has so far mainly been used to identify women with a poor prognosis as candidates for adjuvant therapy but without demonstrated value for therapy prediction.<h4>Methods</h4>We obtained the gene expression profiles of 159 population-derived breast cancer patients, and used hierarchical clustering to identify the signature ...[more]

PMID: 16280042

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Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients

Project description:Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996. Material was frozen immediatley on dry ice or in liquid nitrogen and stored in -70°C freezers. This series contains expression data for n=159 tumors from which RNA could be collected in sufficient amounts and quality for analysis. Keywords: breast cancer, expression profiling, predictive gene signature, molecular classification of cancecr

2006-05-31 | GSE1456 | GEO

Expression data from human sarcoma patient samples treated with either vehicle control or Nutlin-3a

Project description:This study has examined the molecular mechanisms underlying sensitivity of sarcomas to Nutlin-3a, a non-genotoxic activator of the p53 pathway. Human patient material was collected immediately following surgical resection, dissected into small pieces and ex planted onto gelatin sponges immersed in media containing either vehicle control or Nutlin-3a (10uM and/or 50uM) for 48 hours. Nutlin-3a represents a novel targeted therapy for the treatment of sarcomas. We have examined expression profiles of genes upregulated in sarcoma patient derived tissues following nutlin-3a treatment ex vivo 16 samples ((Vehicle control and Nutlin-3a (10uM and 50uM) treated samples)) from 6 sarcoma patients

2014-03-10 | E-GEOD-48296 | biostudies-arrayexpress

OncoScan analysis of breast carcinomas from the Swedish haemangioma cohort

Project description:The Swedish haemangioma cohort consists of 17,200 women treated with radium-226 for skin haemangioma at an early age (<1.5 years of age) between 1920 and 1965. A total of 877 breast cancer cases were reported by December 2009, estimating an excess relative and absolute risk at the age of 50 years of 0.48 Gy^(−1) and 10.4 (10^4 PYR Gy)^(−1), respectively. We screened 31 primary breast carcinomas for genetic alterations using the OncoScan CNV Plus Assay to assess genomic instability.

2019-04-12 | GSE125700 | GEO

Gene expression in obese humans before and during treatment with rimonabant

Project description:Rimonabant was prescribed to eight patients, admitted to the Overweight Study Unit at the Department of Medicine, Karolinska University Hospital. All patients had a BMI > 35 kg/m2, were treated on clinical indications (metabolic and mechanical disability) and without mental disturbances. Blood samples were collected before treatment and at the first clinical control, when the patients had received rimonabant, 20 mg daily, for 4 weeks.

2015-04-21 | GSE68055 | GEO

Homo sapiens

Project description:Biobank of Karolinska Endarterectomy (BiKE)

| PRJNA126209 | ENA

Perceived employability trajectories: A Swedish cohort study.

Project description: Not available

| S-EPMC5557820 | biostudies-other

Transcription profiling of Xenopus epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate cells, either alone or along with FoxJ1

Project description:Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate cells, either alone or along with FoxJ1. FoxJ1 misexpression leads to the induction fo ectopic cilia in Xenopus laevis epithelia. Results show which genes are affected by FoxJ1 during the induction of ectopic cilia. Ciliated cells that produce a leftward fluid flow have been proposed to mediate left-right patterning in many vertebrate embryos. These cilia combine features of primary sensory and motile cilia, but how such cilia are specified is unknown. We address this issue by analyzing the Xenopus and Zebrafish homologs of FoxJ1, a forkhead transcription factor necessary for ciliogenesis in multi-ciliate cells of the mouse. We show that the cilia that underlie left-right patterning on the Xenopus gastrocoel roof plate (GRP) and Zebrafish Kupfferâs vesicle (KV) are severely shortened or fail to form in FoxJ1 morphants. We also show that misexpressing XFoxJ1 is sufficient to induce ectopic GRP-like cilia formation in frog embryos. Microarray analysis indicates that XFoxJ1 induces the formation of cilia by upregulating the expression of motile cilia genes. These results indicate that FoxJ1 is a critical determinant in specifying cilia used in left-right patterning. Experiment Overall Design: 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD alone or along with FoxJ1. At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip. At stage 22 RNA was harvested from explants and used as the starting material for arrays.

2008-10-25 | E-GEOD-12613 | biostudies-arrayexpress

Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown on a synthetic medium

Project description:We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain grown in a synthetic medium at 70Â°C. Keywords: time course Wild-type T. thermophilus HB8 strains were pre-cultured at 70Â°C for 16 h in 3 ml of synthetic medium. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70Â°C. Cells were collected after 360, 480, 600, 720, 840, 960, 1080, 1200, 1320 and 1440 min, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under 'Description' field of each Sample.

2010-10-15 | E-GEOD-19747 | biostudies-arrayexpress

Breast Cancer. Ull-series. 167 samples

Project description:167 Ull-samples 244k array Tumor tissue from a series of 212 primary breast cancers were sequentially collected at Ullevål University Hospital, Oslo, Norway between 1990 and 1994. Tissues were collected at the time of primary surgery and snap frozen. We performed aCGH on 167 of these samples. DNA was isolated using chloroform/phenol extraction, followed by ethanol precipitation. The aCGH-platform was the Agilent Human genome CGH Microarray 244k. The aim of this study was to investigate the genome wide genomic copy number alterations in a cohort of primary breast cancer patients.

2010-07-06 | GSE20394 | GEO

Early downstream targets of Notch signaling which contribute to multiciliate cell fate

Project description:Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate and proton secreting cells or with dominant negative human Mastermind (HMM) or a DNA binding mutant of Mastermind (DBM) to induce the formation of ectopic multi-ciliate and proton secreting cells. Results show which genes are up or down-regulated when DBM/HMM are compared to ICD. Epithelial cells projecting hundreds of motile cilia are prominent in the respiratory system, brain ependyma and female reproductive tract where they generate a vigorous fluid flow along luminal surfaces. Despite their importance for organ function, how multiciliate cells arise developmentally in diverse epithelia is poorly understood. Notch signaling has been shown in a variety of tissues, including the Xenopus epithelium, to regulate the formation of multiciliate cell precursors. In order to identify early downstream targets of Notch signaling which contribute to multiciliate cell fate we blocked or activated Notch signaling in explants of Xenopus epithelium and looked at changes in gene expression to identify candidates that regulate multiciliate cell fate. Here we identify a novel coiled-coil protein, called multicilin (MCI), whose expression is Notch-regulated and restricted to epithelia where multiciliate cells forms in Xenopus embryos. Inhibiting MCI activity blocks the formation of multiciliate cell precursors while ectopic MCI activity is sufficient to induce multiciliate cell differentiation within epithelial progenitors. 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD, DBM or HMM. At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip. At stage 12 RNA was harvested from explants and used as the starting material for arrays.

2012-03-01 | E-GEOD-32331 | biostudies-arrayexpress

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