Gene expression in experimentally injured and control mouse spinal cords
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus Homo sapiens
PROVIDER: GSE27359 | GEO | 2011/02/17
SECONDARY ACCESSION(S): PRJNA137033
REPOSITORIES: GEO
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Project description:This laboratory works on selectins and their carbohydrate ligands in lymphocyte homing and inflammation. The lab also studies heparin-degrading endosulfatases and their roles in regulating the interactions of growth factors and morphogens with proteoglycans.
2011-02-04 | GSE27056 | GEO
Project description:This laboratory works on selectins and their carbohydrate ligands in lymphocyte homing and inflammation. The lab also studies heparin-degrading endosulfatases and their roles in regulating the interactions of growth factors and morphogens with proteoglycans. The purpose of the experiment is to examine gene expression profiles in spinal cords of injured as a function of time after a contusion injury. The tissue will be generated in the lab of Linda Noble, Professor in the Department of Neurological Surgery at UCSF who is an expert on the pathogenesis of spinal cord injury. Wild-type male C57B/6 mice (8-10 weeks of age) were used. Injuries were produced by contusion. Spinal cords from control mice (uninjured) and experimental (injured) mice were processed (4 and 7 days after injury). A 3 mm length of spinal cord (centered at the injury) and a 3 mm segment from a distant site were isolated from each animal. Tissue from 3 mice were pooled for each sample. Three replicate samples per treatment group were processed for RNA. Thus, a total of 18 RNA samples were hybridized to 18 gene chips. The analysis will determine whether specific glycosylation changes accompany spinal cord injury. Of particular interest are changes in the sulfation profile of proteoglycan GAG chains (e.g., chondroitin sulfate) and in the appearance of potential carbohydrate ligands for infiltrating leukocytes bearing L-selectin or other endogenous lectins.
2011-02-17 | E-GEOD-27359 | biostudies-arrayexpress
Project description:This laboratory works on selectins and their carbohydrate ligands in lymphocyte homing and inflammation. The lab also studies heparin-degrading endosulfatases and their roles in regulating the interactions of growth factors and morphogens with proteoglycans. Gene expression profiles from null and doubly null mice for 2 sulfotransferases (HED-GlcNAc6ST and GlcNAc6ST-1) will be compared to WT mice to find impact on L-selectin ligand formation in lymph nodes. RNA was isolated from the lymph nodes of the 2 types of null mice, 1 type of double null mice, and 1 of wild type mice. 3 duplicates of each strain were analyzed by gene expression profiling. We have null mice and doubly null in two sulfotransferases (HEC-GlcNAc6T and GlcNAc6ST-1) involved in L-selectin ligand formation in lymph nodes. Our functional analysis reveal partial loss (50 and 25%)of lymph node L-selectin ligands in the singly null mice and an 80%loss in the double null mice. We want to identify candidates for the protein scaffolds and underlying posttranslational modifications responsible for the residual L-selectin ligand activity in these mice. We will perform a glycochip analysis with mRNA isolated from lymph nodes of the 3 types of null mice and wild-type mice, all on the C57BL/6 background. Three duplicates from each strain are analyzed, requiring a total of 12 chips. The mice are 8-10 weeks of age and all female.
2011-02-04 | E-GEOD-27056 | biostudies-arrayexpress
Project description:Dr. Esko's laboratory focuses on the structure, function, and biosynthesis of glycoproteins and proteoglycans. This laboratory also works on the design and synthesis of small molecule inhibitors of glycosylation. Gene expression in F9 teratocarcinoma cells: Study of the differential expression of glycosyltransferases, sulfotransferases and proteoglycan core proteins in F9 teratocarcinoma cells before and after differentiation with retinoic acid/theophylline/cAMP. Published data indicated that differentiation of the cells induces the synthesis of anticoagulant heparin-like compounds and a large increase in overall glycosaminoglycan synthesis.
2011-03-02 | GSE27592 | GEO
Project description:Dr. Esko's laboratory focuses on the structure, function, and biosynthesis of glycoproteins and proteoglycans. This laboratory also works on the design and synthesis of small molecule inhibitors of glycosylation. Gene expression in F9 teratocarcinoma cells: Study of the differential expression of glycosyltransferases, sulfotransferases and proteoglycan core proteins in F9 teratocarcinoma cells before and after differentiation with retinoic acid/theophylline/cAMP. Published data indicated that differentiation of the cells induces the synthesis of anticoagulant heparin-like compounds and a large increase in overall glycosaminoglycan synthesis. Glyco-gene Chip microarray analysis of RNA samples (in triplicate) from the cells before and after differentiation to reveal factors that regulate the assembly process and how it leads to the generation of binding sites for glycan-binding proteins.
2011-03-02 | E-GEOD-27592 | biostudies-arrayexpress
Project description:BackgroundRecent studies have found that probenecid has neuroprotective and reparative effects on central nervous system injuries. However, its effect on genome-wide transcription in acute spinal cord injury (SCI) remains unknown. In the present study, RNA sequencing (RNA-Seq) is used to analyze the effect of probenecid on the local expression of gene transcription 8 h after spinal injury.MethodsAn Infinite Horizon impactor was used to perform contusive SCI in mice. The SCI model was made by using a rod (1.3 mm diameter) with a force of 50 Kdynes. Sham-operated mice only received a laminectomy without contusive injury. The injured mice were randomly assigned into either the control (SCI_C) or probenecid injection (SCI_P) group. In the latter group, the probenecid drug was intraperitoneally injected (0.5 mg/kg) immediately following injury. Eight hours after the injury or laminectomy, the spinal cords were removed from the mice in both groups. The total RNAs were extracted and purified for library preparation and transcriptome sequencing. Differential gene expressions (DEGs) of the three groups-sham, SCI_C and SCI_P-were analyzed using a DESeq software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed using a GOseq R package and KOBAS software. Real-time quantitative reverse-transcriptase polymerase chain reaction was used to validate RNA-Seq results.ResultsRNA-Seq showed that, compared to the SCI_C group, the number of DEGs was 641 in the SCI_P group (286 upregulated and 355 downregulated). According to GO analysis, DEGs were most enriched in extracellular matrix (ECM), collagen trimer, protein bounding and sequence specific DNA binding. KEGG analysis showed that the most enriched pathways included: cell adhesion molecules, Leukocyte transendothelial migration, ECM-receptor interactions, PI3K-Akt signaling pathways, hematopoietic cell lineages, focal adhesions, the Rap1 signaling pathway, etc. The sequence data have been deposited into the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra/PRJNA554464).
| S-EPMC6944129 | biostudies-literature
Project description:Dr. Esko's laboratory focuses on the structure, function, and biosynthesis of glycoproteins and proteoglycans. This laboratory also works on the design and synthesis of small molecule inhibitors of glycosylation.
2011-02-17 | GSE27351 | GEO
Project description:Dr. Esko's laboratory focuses on the structure, function, and biosynthesis of glycoproteins and proteoglycans. This laboratory also works on the design and synthesis of small molecule inhibitors of glycosylation. We analyzed the expression patterns of glycosyltransferase, growth factors, and receptors in endothelial cells derived from NDST1 deficient and wild-type mice using cancer cell line types U937 and LS180 .
2011-02-17 | E-GEOD-27351 | biostudies-arrayexpress
Project description: Not available
| S-EPMC6690136 | biostudies-literature
Project description:Spinal cord injury (SCI) is a serious condition that results in disability and has a high morbidity rate; its treatment is very difficult. Although troxerutin and cerebroprotein hydrolysate (TCH) injections have been extensively used in clinics in China for the treatment of traumatic brain injury (TBI) and cerebral stroke, the potential efficacy of TCH injection in the treatment of SCI has never been revealed. In this study, the effects of administering TCH injections on neurological recovery in post-SCI rats were first tested with regard to the behavior and histology; subsequently, the specific expression profile of mRNAs and long noncoding RNAs (LncRNAs) in their spinal cords were conducted using RNA sequencing (RNA-seq). The LncRNA-mRNA networks were also elucidated. After SCI, we found that TCH injection with the right dose is effective for the recovery of locomotion function and repairing of the damaged tissue in the spinal cord; TCH injection is also discovered to have a role in the regulation of 443 differentially expressed genes (DEGs) and 27 differentially expressed LncRNAs (DELs) that are identified to have multiple functions, including locomotion, blood vessel morphogenesis, thiamine metabolism, Hippo signaling pathway, and axon guidance, by applying the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) analysis. In addition, it is revealed that, after SCI, the highly expressed LncRNA AABR07071383.1 in the post-SCI cis/trans-regulates the expression of mRNA Acpp mRNA that encodes a key enzyme involved in the metabolic process of thiamine in the abirritation of the dorsal root ganglion (DRG), which implies that TCH injection may be more effective when administered with benfotiamine (a common treatment drug).
| S-EPMC7424371 | biostudies-literature