Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each sample was made from pooling 4 distinct animals. Sample preparation and hybridization were performed by UCL genomics, following Affymetrix instructions. The 6 replicates were also used for RNA-seq, see GSE53762.
Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each sample was made from pooling 4 distinct animals. Sample preparation and hybridization were performed by UCL genomics, following Affymetrix instructions. The 6 replicates were also used for RNA-seq, see GSE53762.
Project description:Analysis of whole mouse brain following peripheral, cutaneous immune stimulation with Aldara cream or aquaeous control cream. Results provide insight into the central response to peripheral inflammation Microarrays were used to investigate the global gene expression of mouse brains following peripheral, cutaneous application of Aldara cream or control cream C57BL/6 mice were treated with 80mg topical Aldara cream or aquaeous control cream every 24 hours for 5 consecutive days. 24 hours following the final application, brains were removed and RNA was extracted using RNeasy Mini Kit (Qiagen). 5 brains from each group were analysed using full genome Affymetrix GeneChip array
Project description:Alternative splicing of pre-mRNA generates protein diversity and has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantication of expression levels for the majority of exons and facilitates the discovery of alternative splicing events. Analysis of exon array data is more challenging than gene expression data and there is a need for reliable quantication of exons and alternative spliced variants. We introduce a novel, computationally efficient methodology, MEAP, for exon array data preprocessing, analysis and visualization. We compared MEAP with other preprocessing methods, and validation of the results show that MEAP produces reliable quantication of exons and alternative spliced variants. Analysis of data from head and neck squamous cell carcinoma (HNSCC) cell lines revealed several variants associated with 11q13 amplication, which is a predictive marker of metastasis and decreased survival in HNSCC patients. Together these results demonstrate the utility of MEAP in suggesting novel experimentally testable predictions. Thus, in addition to novel methodology to process large-scale exon array data sets, our results provide several HNSCC candidate genes for further studies. We analyzed 15 samples using the Affymetrix Human Exon 1.0 ST platform, of which 7 samples have 11q13 amplification. Array data was preprocessed by using Multiple Exon Array Processing (MEAP).
Project description:In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations. Exon level expression on 176 HapMap cell lines.
Project description:Analysis of the effects of three members of the FGF family (FGF1, FGF2 and FGF9) and bone morphogenic protein 4 (BMP4) on myelinating cultures generated from dissociated embryonic spinal cord. The results of both immediate (24 hours, T1 (24 hrs)) and long term treatments (10days, T2) give insights into the cumulative effects of sustained FGF and BMP mediated signal transduction in the pathogenesis of demyelinating diseases. Dissociated myelinating cultures were generated from neurosphere derived astrocytes (generated from striata of P1 Sprague-Dawley rats) and spinal cord cells from E15.5 Sprague-Dawley(SD) embryos. The effect of recombinant human FGF9 and other soluble factors on these in vitro myelinating cultures was investigated by adding them to the culture media after 18 days in vitro (DIV). The effects of each factor were analysed using three independent cultures at two time points (19DIV and 28 DIV).
Project description:Failure of remyelination in multiple sclerosis (MS) is associated with inhibition of oligodendrocyte precursor (OPC) differentiation, but the cellular and molecular mechanisms involved remain poorly understood. We now report inflammatory demyelination in MS is associated with localized expression of fibroblast growth factor 9 (FGF9) by oligodendrocytes and to a lesser extent astrocytes, and demonstrate FGF9 inhibits myelination and remyelination in vitro. This inhibitory activity is reversible and due to an off target FGF9-dependent effect on astrocytes that disrupts in the growth factor milieu required to support myelination. We identify multiple downstream events induced by FGF9 associated with this effect including increased expression of leukaemia inhibitory growth factor (LIF) and FGF2, both of which are shown to inhibit myelination if present in excess. These studies identify FGF9-dependent signal transduction in astrocytes as a novel target for therapeutic strategies designed to enhance remyelination by endogenous OPC in MS. Gene expression profiles of rat myelinating cultures grown in the presence or absence of FGF9 (100 ng/ml) for 24h and 10 days were generated using Affymetrix GeneChip® Rat Gene 1.0 ST Arrays. Each time point (T1: 24 hrs, and T2: 10 days) has Control (CTR) and Treatment (FGF) groups, with two replicates in each group. In total, 8 arrays were generated from the four groups (CTR-T1, CTR-T2, FGF-T1 and FGF-T2).
Project description:A transcriptome signature which discriminate efficiently primary and radiation induced breast angiosarcomas can be generated from FFPE tumor samples.FFPE samples are good material to unlock relevant informations from tumors. The transcriptome of 35 FFPE breast angiosarcomas (10 primary and 25 radiation induced) were analysed using Affymetrix Human Exon 1.0 ST arrays according to the FFPE dedicated protocole from NuGEN and compared to paired fresh frozen samples previously analysed. FF Samples are also available in Array Express as E-MEXP-3252.
Project description:This data set was generated by the UK Brain Expression Consortium and consists of gene expression data generated from post-mortem human brain samples, dissected from 10 brain regions and originating from a large cohort of neurologically and neuropathologically normal individuals. The UK Brain Expression Consortium has generated gene expression data on a large cohort of neurologically and neuropathologically normal individuals in order to better understand gene expression differences across the human brain. 1231 samples are analysed in total and these samples originate from 134 Caucasian individuals. From each individual, up to ten brain regions were sampled and analysed.