Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

57 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression analysis of CALGB 9741 patient tumor samples using the nCounter RUO-PAM50 signature

ABSTRACT: Intrinsic subtyping of breast cancer was performed using an nCounter RUO-PAM50 gene expression assay to determine the ability of instrinsic subtyping to predict what patients may benefit from altered chemotherapy scheduling in the CALGB 9741 clinical trial population. FFPE primary breast tumor samples archived at the CALGB Pathology Coordinating Office (PCO) were used to obtain total RNA for instrinsic subtyping using the nCounter Analysis System. Gene-expression profiles were generated for 1321 of 1471 patient samples (90%) suitable for inclusion in this study.

ORGANISM(S): Homo sapiens

SUBMITTER: Sherri Davies

PROVIDER: E-GEOD-74821 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression of DNA repair and cell cycle genes in a cohort of primary and recurrent glioblastoma multiforme patients

Project description:Direct mRNA counting of 154 DNA repair and cell-cycle genes in a cohort of paired GBM patients using the nCounter technology (Nanostring)

2019-03-13 | E-MTAB-6425 | biostudies-arrayexpress

RNA profiling from ovarian FFPE specimens (Nanostring)

Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from ovarian cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. five serous carcinoma and six clear cell carcinoma samples with technical replicates

2014-07-01 | E-GEOD-55056 | biostudies-arrayexpress

RNA profiling from prostate FFPE specimens (Nanostring)

Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. five paired tumor and adjacent normal prostate tissue speciemens with technical replicates

2014-07-01 | E-GEOD-55055 | biostudies-arrayexpress

NanoString assays of miRNA in MCF7 and MCF10A cells and in extracellular vesicles (EVs) derived from these cells.

Project description:The goal of this study is to identify unique miRNA profiles of EVs from MCF7 and MCF10A cells that distinguish their cellular origin. 654 human mature miRNAs were analyzed in NanoString assays to identify miRNA with high abundance in MCF7 EVs and the greatest fold change for MCF7 EVs relative to MCF10A EVs.

2015-02-21 | E-GEOD-66165 | biostudies-arrayexpress

Using Mass Cytometry and In vivo Imaging to Study Emergency Repopulation of Immune Cells in Murine Liver

Project description:Macrophages and dendritic cells are phagocytes present in almost all tissues in mammals and play a pivotal role for tissue homeostasis and during immune responses. Liver phagocytes play a pivotal role in host immune responses and exquisite mechanisms are necessary to govern the density and the location of the different hepatic leukocytes. However in catastrophic events including trauma, infections or toxin ingestion, many of the liver phagocytes can be wiped out leaving large areas devoid of these cells. Here we used a unique combination of mass cytometry (CyTOF), gene expression and liver intravital approaches to precisely determine phagocytic populations within the liver and the functional consequences of their replenishment by myeloid precursors. While Kupffer cells were exclusively located in the sinusoidal lumen, we identified a population of dendritic cells that was mainly located under the liver capsule. After full depletion of dendritic and Kupffer cells, intravascular myeloid precursors replenished location, density and function of both populations. However, these emergency repopulated livers were dysfunctional in their ability to respond to injury and to clear bacteria for at least 30 days. After this âeducational periodâ, new phagocytes returned to normal response to injury and bacterial trapping. Conclusions: Our data shed light on the liverâs ability to locally shape phagocyte precursors into two vastly different immune cells localized to two fundamentally different tissue compartments. 4 different cell types were isolated from mice, RNA was extracted, and gene expression was measured using the Nanostring nCounter Mouse Immunology Panel

2016-06-12 | E-GEOD-81645 | biostudies-arrayexpress

Repeatability and comparability of microRNA microarray

Project description:We compared repeatability and comparability of microRNA microarray using 5 different platforms. and compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR. Our data suggested that the most accurate and repeatable methods for microRNA expression profiling are Agilent and Toray, and the numbers of detected microRNA at Toray are more than at Agilent. Keywords: repeatability, comparability, microRNA, microarray We compared repeatability and comparability of microRNA microarray using 5 different platforms (Agilent, Ambion, Exiqon, Invitrogen, and Toray). In addition, we compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR.

2010-05-19 | E-GEOD-13860 | biostudies-arrayexpress

Gene expression analysis of CALGB 9741 patient tumor samples using the nCounter RUO-PAM50 signature

Project description:Intrinsic subtyping of breast cancer was performed using an nCounter RUO-PAM50 gene expression assay to determine the ability of instrinsic subtyping to predict what patients may benefit from altered chemotherapy scheduling in the CALGB 9741 clinical trial population.

2015-11-10 | GSE74821 | GEO

Concordance of PAM50 molecular subtyping between oligonucleotide microarray and NanoString nCounter assay for Taiwanese breast cancer

Project description:Five molecular subtypes have been identified according to intrinsic genes transcription. Microarrays have been adopted for molecular subtyping in addition to the original NanoString nCounter assay. This study aimed to evaluate subtyping consistency among Taiwanese breast cancers. Our study showed that fundamental discrepancy exists between distinct gene expression measuring approaches, and cross platform equivalence should not be overemphasized with too much extrapolation.

2021-09-01 | GSE162228 | GEO

miRNA Microarray Profiling of Nine Different Normal Human Tissues

Project description:We measured the expression of 470 human miRNAs in nine human tissues using Agilent DNA microarrays. miRNA microarrays were manufactured by Agilent Technologies (Santa Clara, CA), and contain 20-40 features targeting each of 470 human miRNAs (Agilent design ID 016436). Sequences of the 470 miRNAs were obtained from the Sanger miRBase, release 9.1. Labeling and hybridization of total RNA samples were performed according to the manufacturer’s protocol. 100ng total RNA was used as input into the labeling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C. The labeling and hybridizations of the nine human tissues were done 4-5 times using the same starting RNA sample for each tissue.

2008-08-19 | E-GEOD-11806 | biostudies-arrayexpress

microRNA expression in human hepatitis c virus (HCV) liver biopsy samples

Project description:In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all microRNA profiles. This series includes microRNA profiles of 36 samples, 24 HCV positives and 12 HCV negatives.

2010-05-06 | E-GEOD-15288 | biostudies-arrayexpress

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