RNA sequencing analysis of the sea lamprey brainstem after spinal cord injury and GABA or baclofen treatments
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PROVIDER: PRJNA573684 | ENA |
REPOSITORIES: ENA
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Project description:We have previously shown that GABA ainhibits caspase activation and promote axon regeneration in descending neurons of the sea lamprey brainstem after a complete spinal cord injury. Here, we repeated this treatment and performed Illumina RNA sequencing studies in the brainstems of control and GABA treated animals.
2019-09-24 | GSE137859 | GEO
Project description:We have previously shown that baclofen treatments inhibit caspase activation and promote axon regeneration in descending neurons of the sea lamprey brainstem after a complete spinal cord injury. Here, we repeated this treatment and performed Illumina RNA sequencing studies in the brainstems of control and baclofen treated animals.
2019-09-24 | GSE137858 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-09-24 | GSE137860 | GEO
Project description: Not available
| S-EPMC7354674 | biostudies-literature
Project description:Brainstem control of transcription after spinal cord injury (SCI)
| PRJNA549934 | ENA
Project description:The spinal cord after injury shows altered transcription in numerous genes. We tested in a pilot study whether the nucleus raphé magnus, a descending serotonergic brainstem region whose stimulation improves recovery after incomplete spinal cord injury, can influence these transcriptional changes. Rats received 2 hours of low-frequency electrical stimulation in the raphé magnus three days after an impact contusion at segment T8. Comparison groups lacked injuries or activated stimulators or both. Immediately following stimulation, spinal cords were extracted, their RNA transcriptome sequenced, and differential gene expression quantified. Confirming many previous studies, injury primarily increased inflammatory and immune transcripts and decreased those related to lipid and cholesterol synthesis and neuronal signaling. Stimulation plus injury, contrasted with injury alone, caused significant changes in 43 transcripts (39 increases, 4 decreases), all protein-coding. Injury itself decreased only four of these 43 transcripts, all reversed by stimulation, and increased none of them. The non-specific 5-HT7 receptor antagonist pimozide reversed 25 of the 43 changes. Stimulation in intact rats principally caused decreases in transcripts related to oxidative phosphorylation, none of which were altered by stimulation in injury. Gene ontology (biological process) annotations comparing stimulation with either no stimulation or pimozide treatment in injured rats highlighted defense responses to lipopolysaccharides and microorganisms, and also erythrocyte development and oxygen transport (possibly yielding cellular oxidant detoxification). Connectivity maps of human orthologous genes generated in the CLUE database of perturbagen-response transcriptional signatures showed that drug classes whose effects in injured rats most closely resembled stimulation without pimozide include peroxisome proliferator-activated receptor agonists and angiotensin receptor blockers, which are reportedly beneficial in spinal cord injury. Thus, the initial transcriptional response of injured spinal cord to raphé magnus stimulation is upregulation of genes that in various ways are mostly protective, some probably located in recently arrived myeloid cells.
2019-11-03 | GSE133093 | GEO
Project description:The lamprey is a vertebrate that, unlike mammals, achieves spontaneous recovery after spinal cord transection. Despite anatomical, physiological, and behavioral data on spinal cord regeneration in lamprey, the molecular mechanisms underlying this capacity are largely unknown. To address this, we used RNA-Seq to obtain transcriptional profiles from uninjured animals and at 10 time points ranging from 6 hours to 12 weeks post injury. Overall, 4208 (spinal cord) and 3788 (brain) transcripts are differentially expressed (DE). Complex intraspinal and supraspinal responses were induced acutely and occurred even at chronic phases of recovery. Leveraging functional data for mammalian homologs of DE genes (via Enrichr) permitted identification of enriched conserved genes and pathways. These included genes and pathways induced after mammalian peripheral nerve injury, such as those associated with regeneration, immune function, cell growth, proliferation and cell death. For example, ATF3, a transcription factor implicated in mammalian peripheral nerve regeneration, is highly expressed and enriched in lamprey spinal cord and brain after SCI. Other homologs of regeneration-associated genes that are differentially expressed after SCI include members of the WNT, HDAC, SOX, SMAD, KLF, and JUN families. This study provides the first comprehensive view of transcriptional responses during successful anatomical and functional recovery from spinal cord injury in lamprey, and reveals unexpectedly large changes in transcription in the brain, which is quite distant from the spinal lesion site. Gene expression patterns associated with functional recovery in lamprey may be useful in guiding studies aimed at modulating mammalian responses to SCI.
2018-03-03 | GSE95686 | GEO
Project description:au05-03_gaba - ler vs pop2-1: gaba over-accumulation effects - The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition. Designed experiment consisted in comparison of transcriptomes of Arabidopsis thaliana Landsberg erecta ecotype and its mutant pop2-1 (impaired in GABA transaminase activity) during a kinetic of endogenous GABA accumulation. For this purpose, 10-day-old plants grown on half strength Hoagland's agar medium were transferred to agar plates supplemented with 1 mM GABA. We isolated RNA from plants treated for 0, 1 and 4 days. Treatments were made in duplicate. Keywords: gene knock-out, time course 6 dye-swap - CATMA arrays
2009-04-11 | E-GEOD-11129 | biostudies-arrayexpress
Project description:We performed a microarray analysis of auditory midbrain (inferior colliculus, IC) mRNA from young adult CBA mice (controls) with good hearing, middle aged (MA) with good hearing, and old mild (MP) and severe (SP) presbycusic CBA mice. Fold Change data derived from RMA normalization revealed that the overall GABA receptor alpha 6 expression profiles for MA, MP and SP were down-regulated relative to young adult controls with good hearing. Relative real-time PCR for five GABA receptors confirmed this age-related down regulation quantitatively. Functional hearing data: Auditory Brainstem Responses (ABR) enriched the analysis to select the probe-sets that changed with age and hearing loss by the linear regression best-fit line model technique. GABA receptor genotype-phenotype correlations with auditory functional data indicated that GABA-receptor subtypes are under expressed in SP mice. Hierarchical clustering (HC) analyses yielded statistical significance of normalized GeneChip data Real-time PCR showed that Gabra6, GABA B receptor 1 (Gabbr1), and Gaba transporter protein Slc32a1 may be involved in physiological changes that occur in age-related hearing loss. Presbycusis – age-related hearing loss – is the number one communicative disorder of our aged population. In this study we analyzed gene expression for a set of GABA receptors in the inferior colliculus of aging CBA mice using the Affymetrix GeneChip MOE430A. Functional phenotypic hearing changes from RMA normalized microarray data (39 replicates) in four age-groups, Young Controls and Middle aged mice with good hearing, mild and sever e presbycusis from old mice. Fold change gene expression derived from RMA normalized data were first subjected to one-way ANOVA, and then linear regression was performed. The selected gene expression changes were confirmed by relative real-time relative to young adult controls with good hearing. Statistically significant and real time PCR confirmed GABA receptor genes; Gabra6, GABA B receptor 1 (Gabbr1), and Gaba transporter protein Slc32a1, may be involved in physiological changes that occur in age-related hearing loss. Lastly, gene expression measures of each age group were correlated with pathway/network relationships relevant to the inferior colliculus using Pathway Architect, to identify key pathways consistent with the gene expression changes observed In the study of Expression changes in IC GABA receptors in the Auditory Midbrain of young adult and aging presbycusis mice total of thirty nine chips were used. The normal aging mice were in Four groups Young adults Controls with good hearing (8 mice, 8 MOE430A GeneChips), Middle aged group with good hearing ( 17 mice, 17 MOE430A GeneChips), Mild Presbycusis with limited hearing loss (9 mice, 9 MOE430A GeneChips) and Severe Presbycusis (5 mice, 5 MOE430A GeneChips).
2013-08-06 | E-GEOD-49522 | biostudies-arrayexpress
Project description:au05-03_gaba - ler vs pop2-1: gaba over-accumulation effects - The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition. Designed experiment consisted in comparison of transcriptomes of Arabidopsis thaliana Landsberg erecta ecotype and its mutant pop2-1 (impaired in GABA transaminase activity) during a kinetic of endogenous GABA accumulation. For this purpose, 10-day-old plants grown on half strength Hoagland's agar medium were transferred to agar plates supplemented with 1 mM GABA. We isolated RNA from plants treated for 0, 1 and 4 days. Treatments were made in duplicate. Keywords: gene knock-out, time course
2009-04-11 | GSE11129 | GEO