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RNA-seq of laser micro-dissected cartilage after surgical induction of osteoarthritis in increased ER stress mice

ABSTRACT: RNA-seq of laser micro-dissected cartilage after surgical induction of osteoarthritis in increased ER stress mice

PROVIDER: PRJEB34089 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3489180_1.fastq.gz	Fastqsanger.gz
	ERR3489180_2.fastq.gz	Fastqsanger.gz
	ERR3489181_1.fastq.gz	Fastqsanger.gz
	ERR3489181_2.fastq.gz	Fastqsanger.gz
	ERR3489182_1.fastq.gz	Fastqsanger.gz

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RNA-seq of laser micro-dissected cartilage after surgical induction of osteoarthritis in increased ER stress mice

Project description:Osteoarthritis was induced in male wild-type and ColIITgcog (c/c) mice by destabilisation of the medial meniscus (DMM). c/c mice have increased ER stress in chondrocytes via the collagen II promoter driven expression of a misfolding protein, the cog form of thyroglobulin. RNA-sequencing of laser micro-dissected cartilage was performed at 2 weeks post-surgery (n=3/group).

2019-08-31 | E-MTAB-8266 | biostudies-arrayexpress

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Project description:RNA-seq of laser micro-dissected cartilage after surgical induction of osteoarthritis in increased ER stress mice

2019-09-09 | E-MTAB-8266 | ExpressionAtlas

Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Project description:The aim of this BBSRC-funded project is to develop laser-capture microdissection (LCMD) to isolate small cell clusters in different regions of arabidopsis embryos at different stages of development; to develop RNA amplification procedures on dissected tissue sampes; and to use DNA microarray techniques to investigate global transcriptional differences between samples. Cryosectioned embryos of ecotype Col-O of globular, heart and torpedo stage were used to isolate cell clusters from the apical and basal regions, for RNA isolation and amplification. !Samples will be provided as T7-primed cDNA, with three biological replicates for each tissue to be analysed. Each replicate comprises cDNA from pooled tissue samples from ca. 15 embryos. The experimental details have been discussed with Sean May et al. at NASC. Experimenter name = Stuart Casson and Matthew Spencer Experimenter phone = 0191 374 7356 Experimenter fax = 0191 374 2417 Experimenter institute = Durham University Experimenter address = Integrative Cell Biology Laboratory Experimenter address = School of Biological Sciences Experimenter address = Durham University Experimenter address = South Road Experimenter address = Durham Experimenter zip/postal_code = DH1 3LE Experimenter country = UK Keywords: organism_part_comparison_design; development_or_differentiation_design

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Transcriptional analysis of micro-dissected articular cartilage in post-traumatic murine osteoarthritis.

Project description:ObjectiveIdentify gene changes in articular cartilage of the medial tibial plateau (MTP) at 2, 4 and 8 weeks after destabilisation of the medial meniscus (DMM) in mice. Compare our data with previously published datasets to ascertain dysregulated pathways and genes in osteoarthritis (OA).DesignRNA was extracted from the ipsilateral and contralateral MTP cartilage, amplified, labelled and hybridized on Illumina WGv2 microarrays. Results were confirmed by real-time polymerase chain reaction (PCR) for selected genes.ResultsTranscriptional analysis and network reconstruction revealed changes in extracellular matrix and cytoskeletal genes induced by DMM. TGFβ signalling pathway and complement and coagulation cascade genes were regulated at 2 weeks. Fibronectin (Fn1) is a hub in a reconstructed network at 2 weeks. Regulated genes decrease over time. By 8 weeks fibromodulin (Fmod) and tenascin N (Tnn) are the only dysregulated genes present in the DMM operated knees. Comparison with human and rodent published gene sets identified genes overlapping between our array and eight other studies.ConclusionsCartilage contributes a minute percentage to the RNA extracted from the whole joint (<0.2%), yet is sensitive to changes in gene expression post-DMM. The post-DMM transcriptional reprogramming wanes over time dissipating by 8 weeks. Common pathways between published gene sets include focal adhesion, regulation of actin cytoskeleton and TGFβ. Common genes include Jagged 1 (Jag1), Tetraspanin 2 (Tspan2), neuroblastoma, suppression of tumourigenicity 1 (Nbl1) and N-myc downstream regulated gene 2 (Ndrg2). The concomitant genes and pathways we identify may warrant further investigation as biomarkers or modulators of OA.

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Expression analysis of laser-dissected SNpc neurons in Parkinson's disease

Project description:Genome-wide transcriptome analysis of expression changes in laser-dissected SNpc neurons from Parkinson's disease brain tissue versus control brain tissue. Post-mortem brain expression analysis performed in 10 PD brain samples and 8 control brain samples.

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RNA-seq of laser-captured dissected endometrium of WT and Thra1 PV/+ mice

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