Time dependent gene expression post SNL in IPSA vs Contralateral DRGs
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ABSTRACT:
PROVIDER: PRJNA799356 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17695263.fastq.gz | Fastqsanger.gz | |||
| SRR17695264.fastq.gz | Fastqsanger.gz | |||
| SRR17695265.fastq.gz | Fastqsanger.gz | |||
| SRR17695266.fastq.gz | Fastqsanger.gz | |||
| SRR17695267.fastq.gz | Fastqsanger.gz |
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Project description:Chronic pain can be debilitating, and current treatments are neither universally efficacious, nor without risks. New therapeutic options are needed. Transient receptor potential (TRP) ion channels regulate inflammation and pain. Understanding how endogenous TRP ligands regulate inflammation and pain may provide insights for new therapies. Spinal nerve ligation (SNL) injury was used as a model for chronic pain. Transcriptomic and targeted lipidomic analysis of damaged tissue revealed time-dependent increases in Cyp1b1 mRNA and a concurrent accumulation of 8,9-EET and 19,20-EpDPA post injury. Production of 8,9-EET and 19,20-EpDPA by human CYP1B1 and mouse Cyp1b1 was confirmed in vitro. 8,9-EET and 19,20-EpDPA selectively and dose-dependently sensitized and activated TRPA1 in overexpressing HEK-293 cells and Trpa1-expressing/AITC-responsive cultured mouse peptigergic DRG neurons. Activation of TRPA1 was attenuated by the antagonist A967079, and mouse Trpa1 was more responsive to agonists including 8,9-EET and 19,20-EpDPA than human TRPA1. This latter effect was mediated in part by amino acids Y933, G939, and S921. Intra-plantar injection of 19,20-EpDPA induced acute mechanical, but not thermal hypersensitivity in mice, which was blocked by A967079. Similarly, Cyp1b1 knockout mice displayed a reduced chronic pain phenotype, indicating a role for Cyp1b1-derived oxylipins in promoting Trpa1 activation and pain. Manipulation of the CYP1B1-oxylipin-TRPA1 axis following nerve injury could have therapeutic benefit.
2023-02-01 | GSE194174 | GEO
Project description:RNA Sequencing of WT Chronic Stroke Infarcts vs. Contralateral Cortices
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Project description:Expression profiling of L4 and L5 Dorsal Root Ganglion (DRG) in the spinal nerve ligation model of neuropathic pain. The goal of the study was to identify genes involved in neuropathic pain This series of samples comprises of contralateral and ipsilateral L4 and L5 DRG tissue collected 4 weeks after rats underwent a L5 spinal nerve ligation (SNL) or a sham operation with no L5 spinal nerve ligation. This defines 8 groups (i) contralateral L4 DRG from the sham cohort (n=5), (ii) ipsilateral L4 DRG from sham cohort (n=5), (iii) contralateral L4 DRG from SNL cohort (n=5), (iv) ipsilateral L4 DRG from the SNL chort (n=5), (v) contralateral L5 DRG from the sham cohort (n=5), (vi) ipsilateral L5 DRG from sham cohort (n=5), (vii) contralateral L5 DRG from SNL cohort (n=5), (viii) ipsilateral L5 DRG from the SNL cohort (n=5)
2011-10-17 | E-GEOD-24982 | biostudies-arrayexpress
Project description:sham: Control vs. different time point post spinal cord injury
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Project description:We report here a systematic approach to characterize the transcriptional responses of different cells types in the dorsal root ganglion (DRG) to peripheral nerve injury using single cell RNA sequencing (scRNAseq). We compare scRNAseq datasets of lumbar DRGs form naïve mice with corresponding datasets from mice subjected to spared nerve injury (SNI) 7 or 14 days prior to analysis. SNI surgery was performed in the left and right hindleg and development of mechanical allodynia was monitored by von Frey testing relative to control mice and the baseline level. Mice were perfused with PBS prior to extraction of L3 and L4 DRGs and DRGs were enzymatically and mechanically dissociated to single cell suspension before scRNAseq. Analysis of transcriptional changes in this nerve injury-paradigm reveals a differential response at 7 days versus 14 days post injury, suggesting dynamic gene modulation over time.
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Project description:AIM: We performed RNA-sequencing experiments seeking genes whose expression changed due to nerve injury. In addition, we wanted to test whether inhibition of the methyl transferase G9a/GLP, that methylates H3K9me2, could reverse those expression changes due to nerve ligation. G9a/GLP methylase was pharmacologically inhibited using UNC0638. METHOD: We generated cDNA libraries from RNA purified from DRGs obtained from Sham operated (4), SNL (4), and SNL plus UNC0638 (3) rats. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the rat genome rn4 using TopHat RESULTS: We were able to map 16876 genes, from which 2035 changed their expression values at least two fold when we compared SNL to Sham operated (pâ?¤ 0.01). There were 1205 upregulated and 832 down-regulated genes. Next, we focused on genes whose expression was either up or down-regulated 2 fold due to nerve ligation, and the values would be normalized to control level after G9a/GLP inhibito (UNC0638)r treatment. We identified 639 genes in our data set that behave this way We generated cDNA libraries from RNA purified from DRGs obtained from Sham operated (4), SNL (4), and SNL plus UNC0638 (3) rats. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the rat genome rn4 using TopHat
2015-11-02 | E-GEOD-59043 | biostudies-arrayexpress
Project description:Early changes in the transcriptome associated with lens wounding in an ex vivo post-cataract surgery chicken model. Here we report the changes in the transcriptome that occur 1hr vs. time 0 post-cataract surgery wounding. Our data provide a molecular framework for understanding the early gene changes associated with the injury response of the lens.
2023-11-04 | GSE239368 | GEO
Project description:Current study aimed to identify the gene expression change that are unique in injured Fmn2-/- DRGs compared with WT mice.
2023-12-31 | GSE243896 | GEO
Project description:CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle
2009-12-31 | GSE12743 | GEO
Project description:We conducted bulk RNA sequencing on infarcts collected from young adult (3-month-old) mice at 7 weeks after the distal middle cerebral artery occlusion + hypoxia stroke model and compared them to contralateral cortices. As expected, differential expression (DE) analysis revealed marked differences between infarcts and contralateral cortices: 3,930 upregulated and 2,869 downregulated genes. The most significantly upregulated genes, including Lpl, Spp1, Cd36, Mmp2, and Mmp19, and the most highly enriched genes, including Cd5l, Mmp3, Mmp12, and Mmp13, indicate a pronounced disturbance in lipid homeostasis in infarcts at 7 weeks after stroke. In addition to alterations in lipid metabolic processes, the transcriptome also revealed a signature of chronic inflammation at 7 weeks after stroke. We then used IPA software to define upstream regulators and identify altered biological processes based on DE analysis. Differentially expressed genes were associated with the following upregulated biological processes: (i) atherosclerosis signaling, (ii) IL-1 signaling, (iii) inflammasome pathway, (iv) eicosanoid signaling, (v) B cell receptor (BCR) signaling, and (vi) phospholipases, along with others. IPA also identified lipid metabolic upstream regulators such as cholesterol, phospholipids, and LDL, as well as immunological upstream regulators such as MYD88, IL18, CD3, IL1B, TLR4, and TNF. These altered biological processes indicate that the stroke infarct transcriptome is characterized by chronic inflammation, dysregulated lipid metabolism, and impaired or absent neuronal function at 7 weeks after stroke.
2021-04-30 | GSE173544 | GEO