RNA profiling from prostate FFPE specimens (Nanostring)
Ontology highlight
ABSTRACT: 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
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
Project description:To study feasibility of gene expression profiling from FFPE tissues using NuGen amplified mRNA hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays, 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. We profiled seven paired tumor and adjacent normal prostate tissue samples from three patients with Gleason score 8, one with Gleason score 7 and three with Gleason 6 disease. 11 samples had two or three technical replicates.
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.
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. 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.
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)
Project description:The expression level of the 31 genes (ERF-1 (AT4G17500), ERF2 (AT5G47220), ERF5 (AT5G47230), ERF6 (AT4G17490), ERF11 (AT1G28370), ERF8 (AT1G53170), ERF9 (AT5G44210), ERF59 (AT1G06160), ERF98 (AT3G23230), MYB51 (AT1G18570), STZ (AT1G27730), WRKY28 (AT4G18170), WRKY33 (AT2G38470), WRKY15 (AT2G23320), ZAT6 (AT5G04340), WRKY48 (AT5G49520), RAP2.6L (AT5G13330), K11J9.4 (AT5G61590), bHLH (AT2G43140), GATA3 (AT4G34680), GA2OX6 (AT1G02400), GA3OX1 (AT1G15550), GA2OX4 (AT1G47990), GA20OX1 (AT4G25420), EXLB3 (AT2G18660), MPK3 (AT3G45640), RAP2.2 (AT3G14230)) was measured upon mild osmotic stress (25mM mannitol) in the third leaf of wild-type plants during the proliferating (9 days after stratification (DAS)), expanding (15 DAS) and mature (22 DAS) developmental stage. The expanding third leaf (15 DAS) was harvested at a high temporal resolution (20 min, 40 min, 1 h, 2 h, 4 h, 8 h, 12 h, 16 h, 24 h and 48 h), whereas the proliferating and mature leaf tissues were harvested 24h after transfer to control or 25 mM mannitol-containing medium. A detailed expression pattern over time for each gene was generated with the nCounter Nanostring® technology.
Project description:The arterial endothelium’s response to its flow environment is critical to vascular homeostasis. The endothelial glycocalyx has been shown to play a major role in mechanotransduction, but the extent to which the components of the glycocalyx affect the overall function of the endothelium remains unclear. The objective of this study was to further elucidate the role of heparan sulfate as a mechanosensor on the surface of the arterial endothelium, by (1) expanding the variety of shear waveforms investigated, (2) continuously suppressing heparan sulfate expression rather than using a pre-flow batch treatment, and (3) performing microarray analysis on post-flow samples. Porcine aortic endothelial cells were exposed to non-reversing, reversing, and oscillatory shear waveforms for 24 hours with or without continuous heparan sulfate suppression with heparinase. All shear waveforms significantly increased the amount of heparan sulfate on the surface of the endothelium. Suppression of heparan sulfate to less than 25% of control levels did not inhibit shear-induced cell alignment or nitric oxide production, or alter gene expression, for any of the shear waveforms investigated. We infer that heparan sulfate on the surface of porcine aortic endothelial cells is not the primary mechanosensor for many shear-responsive endothelial cell functions in this species. Porcine aortic endothelial cells were exposed to 3 different shear waveforms for 24 hours with or without the addition of 300 mU/ml heparinase III to the flow media. The shear waveforms inculded Non-reversing (15 ± 15 dyne/cm2, 1 Hz), Steady (15 dyne/cm2), or Oscillatory (0 ± 15 dyne/cm2, 1 Hz) shear. Four replicates of each condition were performed for a total of 24 experiments. Each experimental sample was hybridized to an oligonucleotide array along with a standard reference sample (static cells).
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
Project description:The purpose of the experiment was to compare the transcriptional profile of lupus nephritis kidney tissue at a first flare and expression at a repeated lupus nephritis episode. All samples were laser microdissected into glomerular and tubular compartments and samples were ran in different cartridges. Fourteen lupus nephritis patients and ten normal controls (7 for glomeruli) FFPE samples were laser microdissected and then ran into 5 cartridges for glomeruli and 5 cartridges for tubulointerstitium. This dataset is part of the TransQST collection.