Gene expression patterns in allergen-driven CD4 T cell responses from human atopics with or without asthma.
ABSTRACT: PBMC from house dust mite (HDM) sensitized atopics with or without asthma (or nonallergic controls) were cultured in the presence or absence of HDM extract for 24 hours. At the termination of the cultures, immunomagnetic separation was performed to purify CD4 T cells. Gene expression was profiled on microarrays. The study design consisted of 72 subjects, and two experimental conditions (medium control, HDM stimulation).
Project description:PBMC from house dust mite (HDM) sensitized atopics were cultured in the presence or absence of HDM extract for 24 hours. At the termination of the cultures, CD4 T cells were isolated using immunomagnetic separation. Gene expression was profiled on microarrays. The study design consisted of 45 subjects and two conditions (medium control, HDM stimulation).
Project description:Erythroid progenitors purified from EpoRCreR26eYFPADAR1fl/- and EpoRCreR26eYFPADAR1fl/+ control mice were compared for global gene array profiles Each sample was purified from one mouse
Project description:We used microarrays to analyse expression profiles of zebrafish retina after optic nerve crush to identify potential regulatory mechanisms that underpin central nerve regeneration Total RNA extracted from 4 samples (pooling 4 animals) of Zebrafish retinae after performing optic nerve crush (at day 3 post crush) vs 4 samples (pooling 4 animals) of control (unoperated) Zebrafish retinae
Project description:Expression analysis of OS tumors with shRNA knockdown of PTHR1 mouse OS 80 (a Cre:lox OS cell line from Boston) was tagged with firefly luciferase expression construct. They were then infected with either control (renilla luciferase shRNA) or an shRNA that effective knocks-down PTHR1 (PTHR1.358; para-thyroid hormone receptor). The cells were injected with matrigel onto the back flank of Balb/c nu/nu mice and left to grow for 1 month with weekly monitoring of tumour size by in vivo luciferase assay. At 4 weeks the tumours were removed and trizol stored. Whole tumour was ground up and set form micro-array. 6 tumors with shRNA PTHR1 knockdown ; 6 tumors with shRNA control (renilla luciferase shRNA) knockdown
Project description:Purpose: We have used microarrays to identify gene expression profiles that distinguish mouse OS cells from normal pre-osteoblast cells and mature osteoblast cells. Methods: Transcriptional profiles of three cell lines derived from tumors from Osx-Cre p53fl/fl Rbfl/fl (fibroblastic OS) mouse model, and from pre-osteoblast cells (Kusa4b10 mouse bone marrow stromal cell line) and osteoblast cells (derived by in vitro differentiation of the Kusab410 mouse bone marrow stromal cell line) were generated by microarray analysis, each in triplicate, using Affymetrix mouse Gene1.0ST arrays. Transcriptional profiles were analyzed in cell lines derived from tumors from a genetically engineered mouse model of human osteosarcoma (Osx-Cre p53fl/fl Rbfl/fl) and osteoblast cells derived from the Kusa4b10 mouse bone marrow stromal cell line, in the undifferentiated state (pre-osteoblasts) and differentiated state (osteoblasts).
Project description:The aim was to identify pathways and genes that are transcriptionally deregulated in osteosarcoma due to changes in CpG island DNA methylation. In order to identify candidates, we compared low passage cell cultures derived from a mouse model of osteosarcoma to mature osteoblasts derived by in vitro differentiation of the mouse bone marrow stromal cell line, Kusa4b10. Under cell culture osteoblastic differentiating conditions, Kusa4b10 cells acquire a mature osteoblastic phenotype (21 days). A potential role for DNA methylation in directing gene expression changes was established by integrating gene expression data with genome wide DNA methylation maps generated by methyl-DNA binding domain capture and NimbleGen promoter arrays (MBDCap-Chip). 3 cell lines derived from primary tumors from p53 Rb Osterix-Cre:lox OS model, 3 Osteoblasts (differentiated Kusa4b10 cells (21 days under osteoblastic differentiation conditions)
Project description:The precise timing and pathway of memory CD8+ T cells differentiation from naïve T cells have remained undetermined. We found the smaller cell-size and slower cell cycling cells were segregated from the proliferative larger cell-size activated T cell pool at the peak of infection. Gene signature of the smaller cell-size slower cycling cells and the large cell-size proliferative cells was compared to the signature of naïve, effector, central and effector memory CD8+ T cells. Total RNA samples were prepared from sorted populations of larger or smaller cell-sized cells from spleens of influenza virus PR8-OVA-infected mice on day 7 p.i. or from in vitro 7 days culture after stimulation with plate-bound anti-CD3ε (1.0 μg ml−1) and anti-CD28 mAb (0.5 μg ml−1). Effector T-cell control samples were prepared from SIINFEKL (100 ng ml−1) stimulated OT-I cells after 4 days of in vitro culture with rIL-2 (10 ng/ml) and sorted as CD8+CD44hiCD62Llo. Control bona fide effector memory and central memory T cells were sorted from the spleens of PR8-OVA-infected mice on day 42 p.i. Naive cells were sorted as CD8+CD44loCD62Lhi cells from uninfected C57BL/6 mice.
Project description:Human cSki was overexpressed using MIGR1 retrovirus in sorted murine Lin-c-Kit+Sca-1+ cells. Cells were infected and cultured for 2 days after infection prior to isolation of GFP+ve cells and microarray. GFP+ve MIGR1 and cSKI cells were compared. Each sample represents an independent infection with either cSki or MIGR1 Comparison of GFP+ve LKS+ infected with MIGR1 and cSki
Project description:Type I interferons (IFN-I) are crucial for effective antimicrobial defence in the central nervous system (CNS) but also can cause severe neurological disease (termed cerebral interferonopathy) as exemplified by Aicardi-Goutières Syndrome and chronic viral infection. In the CNS, microglia and astrocytes have essential roles in host responses to infection and injury, with both cell types responding to IFN-I. However, the extent to which the IFN-I responses of these cells differ, if at all, is still unknown. Here we determined the global transcriptional responses of astrocytes and microglia to the IFN-I, IFN-alpha. MGCs were prepared from 2–4 day-old C57BL/6 mice. Purified primary astrocytes were obtained from the MGCs by magnetic activated cell sorting using anti-CD11b beads. Microglia were obtained from mixed glial cell cultures by mechanical shaking for 4 h. After treating astrocytes and microglia with IFN-alpha for 12 h, microarray using Affymetrix mouse genome array 430 2.0 array was performed on total RNA extracted from these cells. We found that under basal conditions, each cell type has a unique gene expression pattern reflective of its developmental origin and biological function. Following stimulation with IFN-alpha for 12 h, astrocytes and microglia also displayed a common core response that was characterized by the increased expression of genes required for pathogen detection and elimination. Microglia had a more extensive and diverse response to IFN-alpha with twice the number of genes upregulated (282 vs. 141 genes) when compared with astrocytes. Validation of the findings in vivo further suggested that astrocytes and microglia play important but distinct roles in the development of IFN-alpha-driven cerebral interferonopathies.