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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of mouse sciatic peripheral nerve of injured mouse with implant: control (untreated) vs local delivery of MCC950 (NLRP3inh) vs standard FBR treatment dexamethasone (Dex). .

ABSTRACT: RNA-seq comparing expression profile of peripheral nerve damage and microchannel device implantation repair model: control vs local delivery of MCC950 (NLRP3inh) vs standard FBR treatment dexamethasone (Dex).

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Malwina Prater

PROVIDER: E-MTAB-10293 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Prevention of the foreign body response to implantable medical devices by inflammasome inhibition.

Barone Damiano G DG Carnicer-Lombarte Alejandro A Tourlomousis Panagiotis P Hamilton Russell S RS Prater Malwina M Rutz Alexandra L AL Dimov Ivan B IB Malliaras George G GG Lacour Stephanie P SP Robertson Avril A B AAB Franze Kristian K Fawcett James W JW Bryant Clare E CE

Proceedings of the National Academy of Sciences of the United States of America 20220317 12

SignificanceImplantable electronic medical devices (IEMDs) are used for some clinical applications, representing an exciting prospect for the transformative treatment of intractable conditions such Parkinson's disease, deafness, and paralysis. The use of IEMDs is limited at the moment because, over time, a foreign body reaction (FBR) develops at the device-neural interface such that ultimately the IEMD fails and needs to be removed. Here, we show that macrophage nucleotide-binding oligomerizatio ...[more]

PMID: 35298334

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RNA-seq of mouse sciatic peripheral nerve of uninjured mouse against implantation of a silicon device or peripheral nerve injury.

Project description:Foreign body reaction is one of the most important limiting factors to the clinical translation of implantable bioelectronics. The experiment compares the process of foreign body reaction, following the implantation of a silicon device in a mouse peripheral nerve, to that of peripheral nerve injury, following nerve crushing. Both processes are also compared to a naïve peripheral nerve from an uninjured mouse. The endpoints are day 1, 4, 7, 14 and 28 days.

2022-04-30 | E-MTAB-10294 | biostudies-arrayexpress

Advanced Study of Aortic Pathology (ASAP)

Project description:BACKGROUND: The vast majority of thoracic aortic aneurysms (TAAs) are observed either together with a bicuspid aortic valve (BAV), a common congenital disorder, or in idiopathic cases such as patients with a normal tricuspid aortic valve (TAV). The main objective of our study was to identify shared and unique gene expression properties underlying the aortic dilation of BAV and TAV patients. METHODS AND RESULTS: Tissue biopsies for RNA and histological analyses were obtained from aorta of non-dilated (<40mm) and dilated (>45mm) aorta of BAV and TAV patients (in total 131 patients). Additional controls were from mammary artery of the same patients (n=88) and aorta from transplant donors (n=13). Gene expression profiles generated using Affymetrix Exon arrays were analyzed from controls and from aorta intima-media and adventitia of patients (in total 345 samples). 606 genes in aortic intima-media were found to be differentially expressed with dilation. Of these, only few (<4%) were differentially expressed in both BAV and TAV patients. Gene set enrichment analysis identified cell adhesion and extracellular region gene ontology sets as common features of TAA in BAV and TAV patients. The set of immune response genes was observed to be particularly overexpressed in aortic media of dilated TAV samples. CONCLUSION: The divergent gene expression profiles indicate fundamental differences in TAA etiology of BAV and TAV patients. Immune response activation solely in the aorta media of TAV patients suggests that inflammation is a causal factor of TAA in this patient group. Biobank of patient material. Each tissue sample is from a different patient as indicated by patient ID.

2016-01-15 | E-GEOD-26155 | biostudies-arrayexpress

Gene expression profiling of mouse chronic intestinal inflammation

Project description:Trichuris muris (T. muris) induces chronic colitis in susceptible mouse strains with clinical, histological, and immunological homology to human Crohn's disease. Gene expression profiling was performed on colon tissue of resistant (BALB/c) and susceptible (AKR) mice following T. muris infection.

2013-05-13 | E-MEXP-3098 | biostudies-arrayexpress

Cold acclimation

Project description:Experiment was designed to identify transcriptome changes during cold acclimation of Drosophila melanogaster male flies. Resistance to cold is often measured by recovery times from chill coma, which is induced almost immediately upon exposure to low but non-freezing temperatures (~0C), with flies becoming immobilised and losing motor activity. This paralysis is also ostensibly reversible upon return to normal temperatures, although again there can be longer term effects. Acclimation for increased cold resistance requires exposure periods ranging from hours or days to several weeks at low temperatures between 0C to 12C, and samples were taken during the cold acclimation period (1 hr, 2 hr, 3 hr, 6 hr, 12 hr, 24 hr, 36 hr and 48 hr).

2014-05-01 | E-MTAB-1607 | biostudies-arrayexpress

Heat Hardening

Project description:A common measure of heat resistance in Drosophila is the time it takes a fly to be knocked down by higher temperatures measured in a long knockdown tube or in small glass vials. This heat knockdown process involves gradual paralysis and non-responsiveness to stimuli, usually within half hour duration of constant heat exposure, and is ostensibly reversible upon return to lower temperatures, although there may be long-term fitness effects. Hardening for increased heat resistance requires exposure periods of up to 3 hours at temperatures ranging from 34C to 38C. The experiment was aimed at understanding the heat hardening process and samples were taken during the hardening period (15 minutes, 45 minutes, 1½ hours, 2¼ hours and 3 hours).

2014-05-01 | E-MTAB-1608 | biostudies-arrayexpress

Transcruption profiling of human cerebellum, frontal cortex [BA4, BA9] and caudate nucleus HD tissue experiment

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2009-09-12 | E-GEOD-3790 | biostudies-arrayexpress

Z2491 vs MC58 vs FAM18

Project description:comparison of transcritonal profiling between the 3 strains; Neisseria meningitidis serogroup A (Z2491), Serogroup B (MC58), and Serogroup C (FAM18.

2012-06-15 | E-MEXP-3255 | biostudies-arrayexpress

transcriptional analysis of breast circadian clock

Project description:Circadian clocks drive ~24 hr rhythms in tissue physiology. They rely on transcriptional/translational feedback loops driven by interacting networks of clock complexes.To gain insights into the role of the mammary clock, circadian time-series microarrays were performed to identify rhythmic genes in vivo. Breast tissues were isolated at 4 hr intervals for two circadian (24 hourly) cycles, from mice kept under constant darkness to avoid any light- or dark-driven genes.

2017-12-01 | E-MTAB-5330 | biostudies-arrayexpress

DG vs superficial gonorrhoeae comparisons

Project description:transcription profiles of two groups each containing 5 strains of Disseminated gonorrhoeae (DG) and Undisseminated (superficial) gonorrhoeae (UG) were compared. An additional set of comparisons was done between 4 strains from group one Disseminated gonorrhoeae (DG) and another 4 strains from the same group.

2012-06-15 | E-MEXP-3254 | biostudies-arrayexpress

The type VII secretion system protects Staphylococcus aureus against host-specific fatty acids

Project description:The Staphylococcus aureus type VII secretion system (T7SS) exports several proteins that are pivotal for bacterial virulence. The mechanisms underlying T7SS-mediated staphylococcal survival during infection are nevertheless unclear. Here we show that EsxC, a small secreted effector implicated in bacterial persistence, contributes to S. aureus membrane architecture and fluidity. Interestingly, isogenic mutants lacking EsxC, T7SS effectors (EsxA or EsxB), and the membrane-bound EssC are more sensitive to killing by the host-specific fatty acid, linoleic acid (LA), compared to the wild-type. We demonstrate that LA induces more cell membrane damage in the T7SS mutants, although they do not bind differentially to LA. Membrane lipid profiles show that T7SS mutants are also less able to incorporate LA into their membrane phospholipids. Proteomics analyses of wild-type and mutant cell fractions reveal that, in addition to compromising membranes, T7SS defects readily induce bacterial stress and hamper their response to LA challenge. Together, our findings indicate that T7SS is crucial for S. aureus membrane integrity and homeostasis, which is critical when bacteria encounter antimicrobial fatty acids.

2021-09-08 | PXD013081 | Pride

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