Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lacerated muscle gene expression

ABSTRACT: We investigated the inflammatory gene profile of surgically-repaired lacerated muscles during the recovery phase and examined if it was influenced by the integrity/injury of the IM, intramuscular nerve using 3 lacerated rat muscle models: DN, where the IM-nerve was concomitantly cut; RN, where the IM-nerve was crushed but leaving an intact nerve sheath; and PN, a control where the IM-nerve was preserved intact. After 2, 4 and 8 weeks, the animals were sacrificed and their gastrocnemius muscles were removed and total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini Kit according to manufacturers instructions. Biotin-labelled cRNA probes were synthesized from total RNA by using a TrueLabeling-AMP Linear RNA amplification kit (SABiosciences Corp, Frederick, MD). The labeled cRNA probes were hybridized to oligonucleotide fragments spotted on the gene array membranes. Membranes were washed to remove any unincorporated probe and incubated with alkaline phosphatase-conjugated streptavidin (AP-streptavidin). Relative expression levels of specific genes were detected from signals generated by chemiluminescence from the alkaline phosphatase substrate, CDP-Star. The luminizing blots were used to expose X-ray films and quantified by spot densitometry with the aid of GEArray expression analysis suite (SABiosciences Corp, Frederick, MD). The abundance of each transcript was normalized to the normal un-operated muscle of the opposite limb, and to the housekeeping gene markers on each array (Aldoa, GAPdH and BAS2C). The results were presented as log2-fold expression with PN used as a control, to compare the two different types of nerve injuries (RN and DN).

ORGANISM(S): Rattus Norvegicus

SUBMITTER: Barry Pereira

PROVIDER: E-MTAB-755 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effect of rosiglitazone on adipose gene expression in HSL knockout mice with different diet treatment

Project description:To test whether HSL is required for the supply of intrinsic ligands for PPARg for normal adipose differentiation, HSL-/- and wild type (WT) littermates were fed normal chow (NC) and high fat (HF) diets supplemented with or without rosiglitazone (200 mg/kg) for 16 weeks. The expression of diabetes related genes in the WAT of the animals was analyzed using Oligo GEArray Mouse Diabetes Microarrays (OMM-023, SABiosciences, Frederick, MD). Together with other biochemical and physiological data, our results suggest that one of the mechanisms by which HSL modulates adipose metabolism is by providing intrinsic ligands for PPARg. To examine the changes in gene expression in WAT of WT and HSL-/- mice with rosiglitazone and diet treatment, RNA isolated from 4 animals of each group were used for studies of gene expression profiles using Oligo GEArray Mouse Diabetes Microarrays (OMM-023, SABiosciences, Frederick, MD). Data were analyzed using GEArray Expression Analysis Suite (SABiosciences, Frederick, MD) and SAM programs to comprehensively evaluate the differential gene expression of the various samples.

2012-03-18 | E-GEOD-20588 | biostudies-arrayexpress

Expression data from BM-CD138+, obtained from newly diagnosed Multiple Myeloma patients

Project description:A subanalysis of the GIMEMA-MMY-3006 trial was performed to characterize treatment-emergent peripheral neuropathy (PN) in patients randomized to thalidomide-dexamethasone (TD) or bortezomib-TD (VTD) before and after double autologous transplantation (ASCT) for multiple myeloma (MM). 236 patients randomized to VTD and 238 to TD were stratified according to the emergence of grade M-bM-^IM-%2 PN. Gene expression profiles (GEP) of CD138+ plasma cells were analyzed from 122 VTD-treated patients. The incidence of grade M-bM-^IM-%2 PN was 35% in the VTD arm and 10% in the TD arm (p<0.001). PN resolved in 88% and 95% of patients in VTD and TD groups, respectively. Rates of complete/near complete response, progression-free and overall survival were not adversely affected by emergence of grade M-bM-^IM-%2 PN. Baseline characteristics were not risk factors for PN, while GEP analysis revealed the deregulated expression of genes implicated in cytoskeleton rearrangement, neurogenesis and axonal guidance. In conclusion, in comparison with TD, incorporation of VTD into ASCT was associated with a higher incidence of PN which, however, was reversible in most of the patients and did not adversely affect their outcomes nor their ability to subsequently receive ASCT. GEP analysis suggests an interaction between myeloma genetic profiles and development of VTD-induced PN. 120 samples have been analyzed; the homogeneity of samples has been ensured by the immunomagnetic enrichment procedure: only >90% pure CD138+ cells have been employed.

2014-12-23 | E-GEOD-58133 | biostudies-arrayexpress

re-innervation muscle in nerve crush rats

Project description:Two simulated nerve injury models in the rat tibial nerve were compared: the nerve was either cut (denervated, DN group) or crushed but with the nerve sheath intact (re-innervated, RN group). The control group had a preserved and intact tibial nerve. As the high expression of Myh3, Postn, Col6a1 and Cfi (nerve growth factors), the RN group demonstrated superior re-innervation as well. Both differentially expressed genes (DEGs) and proteins (DEPs) were enriched in the PPAR signaling pathway, as well as the energy metabolism.

2022-04-06 | PXD033031 | iProX

Transcription profiling of human proximal tubular epithelial cells inclubated with 5% plasma from septic patients or healthy volunteers

Project description:proximal tubular epithelial cell apoptosis were incubated with 5% plasma of septic patients or healthy volunteers diluited in RPMI 1640

2008-03-15 | E-MEXP-1510 | biostudies-arrayexpress

Gene expression profiling of chemokines and chemokine receptors on B-cells in chronically HIV-1 infected patients

Project description:From the analysis of all genes included in the array a number of individual genes were identified as dys-regulated in HIV-1 infected patients compared to healthy controls. In particular, increased CXCL13 expression in all individual patient samples. Abstract from publication: HIV-1 infection is associated with B-cell abnormalities such as hypergammaglobulinemia, poor immunisation responses and loss of serological memory. To determine whether altered expression of chemokine receptors and their ligands may play a role in B-cell dysfunctions during HIV-1 infection, the expression of CXCR4, CXCR5 and CCR7 receptors and their respective ligands on CD19+ B-cells were examined in HIV-1 infected patients and controls. We report a decreased CXCR5 expression on B-cells from patients (p<0.05), a phenomenon associated with a low CD4 T-cell count (<350 cells/Âµl). Interestingly, an increased expression of CXCL13, the ligand for CXCR5, was found in peripheral B-cells from HIV-1 infected patients. Moreover upon B-cell activation in vitro, CXCL13 was secreted in culture. In addition, CXCL13 positive B-cells were also found in the lymph nodes of HIV-1 infected patients, but not in control tissue. B-cell migration towards CXCL13, CXCL12 and CCL21, ligands for CXCR5, CXCR4 and CCR7, was also evaluated. In patients with a low CD4 Tcell count, migration towards all ligands was increased. Our findings indicate that altered expression of the chemokine receptor-ligand pair, CXCR5/CXCL13 may participate in the establishment of B-cell dysfunctions during HIV-1 infection. Total RNA was extracted from purified peripheral B-cells from 4 controls and 4 patients.

2010-06-25 | E-GEOD-12597 | biostudies-arrayexpress

Effect of rosiglitazone on adipose gene expression in HSL knockout mice with different diet treatment

2012-03-18 | GSE20588 | GEO

Multiple Nf1 Schwann cell populations reprogram the plexiform neurofibroma tumor microenvironment

Project description:To define alterations early in tumor formation, we studied nerve tumors in neurofibromatosis 1 (NF1), a tumor predisposition syndrome in which affected individuals develop plexiform neurofibroma (PN). These benign tumors are driven by NF1 loss in Schwann cells (SC). By comparing normal nerve cells to PN cells using single cell and bulk RNA sequencing, we identified changes in five SC populations, including a de novo Schwann cell progenitor-like population. Long after Nf1 loss, SC populations developed PN-specific expression of Dcn, Postn, and CD74, and showed dramatic expansion of immune and stromal cell populations; in human PN, immune and stromal cells comprised 90% of cells. Label transfer enabled verification of each SC population and predicted tumor unique patterns of cell-cell communication in each SC population. We identified PROS-AXL, FGF-FGFR, and MIF-CD74 and its effector pathway NFkB as deregulated in NF1 SC populations, including SCP-like cells. Each receptor-ligand pair was predicted to influence surrounding cells in mouse and human. These findings highlight remarkable changes in all PN cells driven by loss of NF1 in multiple types of SCs and identify therapeutic targets for PN.

2022-11-23 | GSE181985 | GEO

Molecular profiling of temporal fossa arachnoid cysts

Project description:The gene expression signature of seven surgically removed intracranial temporal fossa arachnoid cysts was generated with two normal arachnoid membrane samples as control. Briefly, we used the Qiagen RNeasy minikit (QIAGEN GmbH Germany, Qiagen) to extract total RNA. After RNA quality and quantity assessment, we then constructed cDNA with RT-PCR reagents (Applied Biosystems, U.S). Gene expression microarray analysis was performed on the ABI 1700 Expression Array System (Applied Biosystems, U.S) using the Applied Biosystems Chemo luminescent RT-IVT Labeling Kit and Human Genome microarray (Applied Biosystems, U.S). Signal intensities generated with the ABI 1700 Expression Array System (Applied Biosystems, U.S) were imported into the J-Express Pro 2.7 software (MolMine AS, Bergen, Norway), where inter-array quantile normalization was performed to minimize the effect of external variables into the data. All control spots and flagged spots were removed, leaving 33096 gene probes available for analysis. First, we performed an unsupervised hierarchical cluster analysis in which the group belonging of the samples was defined. Second, we used Significance Analysis of Microarrays (SAM) with 400 and 1000 permutations to compare AC and AM samples and generate gene lists of differentially expressed genes between these groups. With SAM the false discovery rate (FDR) of the gene lists was calculated. FDR returned the number of false positive genes present on the gene list. A measure of FDR is the Q value, which conveniently shows an estimation of the FDR in percent. In the current study only genes with a Q value <1.0 % were accepted as being differentially expressed. A quantile normalized data set consisting of 33096 individual gene probes for each sample was subjected to Significance Analysis of Microarrays.

2010-05-16 | E-GEOD-19727 | biostudies-arrayexpress

Gene expression profiling in Acute Myeloid Leukaemia (AML)

Project description:We used total RNA obtained from 97 AML samples, consisting of 6 cytogenetically distinct subtypes, to establish expression level of 27,868 individual human genes. Expression data from ABI Human Genome Survey Microarray were filtered, quantile-normalized and subjected to significance analysis of microarrays. We wanted to identify clusters of genes differentially expressed among AML subtypes.

2019-03-15 | E-MTAB-906 | biostudies-arrayexpress

Transcription profiling of Xenopus dorsal root ganglia conditioned in vitro vs freshly dissected control

Project description:Axonal regeneration is enhanced by prior conditioning peripheral nerve lesions. Here we show that Xenopus dorsal root ganglia (DRGs) with attached peripheral nerves (PN-DRGs) can be conditioned in vitro, thereafter showing enhanced axonal growth in response to neurotrophins, similar to preparations conditioned by axotomy in vivo. In contrast to freshly dissected preparations, conditioned PN-DRGs show abundant neurotrophin-induced axonal growth in the presence of actinomycin D, suggesting synthesis of mRNA encoding proteins necessary for axonal elongation occurs during the conditioning period, and this was confirmed by oligonucleotide micro-array analysis.

2008-04-16 | E-MEXP-1297 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data