RNA sequencing of adult zebrafish spinal cord
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE77025 | GEO | 2017/02/06
SECONDARY ACCESSION(S): PRJNA309293
REPOSITORIES: GEO
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Project description:Adult zebrafish regenerate about half of cerebrospinal axons by six weeks after a complete spinal cord transection. We isolated the two populations of neurons that successfully regenerated their axons versus those that did not and isolated the total RNA. Cerebrospinal neurons from unlesioned animals were also collected to serve as controls. Whole transcriptome microarray was performed to determine axonal regeneration-associated genes. For each condition (regenerated, non-regenerated and control neurons) we had 3 biological replicates that consisted of neurons pooled from 3 to 9 zebrafish. A complete spinal cord transection with Fluororuby retrograde tracing was performed at the 8th vertebra level in adult zebrafish. Fluororuby labeled all the neurons in the brain that project their axons to the 8th vertebra. Three weeks later Fluoroemerald was injected 4mm distally from the spinal cord transection site, thereby labeling all neurons that regenerated their axons to this level. The zebrafish were sacrificed 1 week after Fluoroemerald tracing, brain enzymatically dissociated and cells sorted using fluorescence-activated cell sorter. After sorting the total RNA was extracted, amplified and labeled with biotin and then hybridized to Affymetrix 3' IVT gene expression microarray. Unlesioned fish were traced with Fluororuby at the 8th vertebra level and labeled neurons isolated 1 week after to serve as control for gene expression microarray.
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Project description:The study was designed to identify genes regulated after spinal transection that might contribute to regenerative growth of neurons projecting from the NMLF in Zebrafish. Zebrafish were injured by surgical transection of the spinal cord at 1 mm caudal to the brainstem-spinal cord junction (Injured). Animals receiving sham surgery (identical surgical procedures without transection) served as control (Control). The nucleus of the medial longitudinal fascicle (NMLF) was laser capture microdissected from approximately 30 frozen sections. RNA was prepared, amplified, and run on Affymetrix Zebrafish arrays. Zebrafish were used because they recover swimming function after spinal transection in about 6 weeks. The NMLF has been identified as a prominent group of neurons that descend through the site of injury in the spinal cord and that regenerate after injury. Times were selected to distinguish early events from those in the timeframe of regenerative growth.
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Project description:To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we performed ATAC sequencing datasets of zebrafish spinal cord at 2 weeks after sham injury and after transection.
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Project description:Label-free mass spectrometry-based quantitative proteomics was applied to a larval zebrafish spinal cord injury model, which allows axon regeneration and functional recovery within two days (days post lesion; dpl) after a spinal cord transection in 3 day-old larvae (dpf). Proteomic profiling of the lesion site was performed at 1 dpl and 2 dpl as well as corresponding age-matched unlesioned control tissue (4 dpf as control for 1 dpl; 5 dpf as control for 2 dpl).
2023-09-06 | PXD037590 | Pride
Project description:Adult zebrafish regenerate about half of cerebrospinal axons by six weeks after a complete spinal cord transection. We isolated the two populations of neurons that successfully regenerated their axons versus those that did not and isolated the total RNA. Cerebrospinal neurons from unlesioned animals were also collected to serve as controls. Whole transcriptome microarray was performed to determine axonal regeneration-associated genes. For each condition (regenerated, non-regenerated and control neurons) we had 3 biological replicates that consisted of neurons pooled from 3 to 9 zebrafish.
2015-04-17 | GSE56842 | GEO
Project description:The study was designed to identify genes regulated after spinal transection that might contribute to regenerative growth of neurons projecting from the NMLF in Zebrafish. Zebrafish were injured by surgical transection of the spinal cord at 1 mm caudal to the brainstem-spinal cord junction (Injured). Animals receiving sham surgery (identical surgical procedures without transection) served as control (Control). The nucleus of the medial longitudinal fascicle (NMLF) was laser capture microdissected from approximately 30 frozen sections. RNA was prepared, amplified, and run on Affymetrix Zebrafish arrays.
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Project description:Label-free mass spectrometry-based quantitative proteomics was applied to a larval zebrafish spinal cord injury model, which allows axon regeneration and functional recovery within two days (days post lesion; dpl) after a spinal cord transection in 3 day-old larvae (dpf). Proteomic profiling was performed of the lesion site at 1 dpl in control animals and animals with pdgfrb+ cell-specific overexpression of either zebrafish chondoradherin (chad; chad-mCherry fusion), fibromodulin a (fmoda; fmoda-mCherry fusion), lumican (lum; lum-mCherry fusion) or prolargin (prelp; prelp-mCherry fusion).
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Project description:To identify regulators of spinal cord regeneration, we performed RNA sequencing of zebrafish spinal cord at 1 week after sham injury and after transection.
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Project description:Spinal cord injury leads to impaired motor and sensory functions. After spinal cord injury there is a an initial phase of hypo-reflexia followed by a developing hyper-reflexia, often termed spasticity. Previous studies have suggested a relationship between the reappearence of plateau potentials in motor neurons and the development of spasticity after spinalization. To understand the molecular mechanism behind this phenomenon we examined the transcriptional response of the motor neurons after spinal cord injury. We used a rat tail injury model where a complete transection of the caudal (S2) rat spinal cord leads to an immidate flaccid paralysis of the tail and a subsequent appearence of spasticity 2-3 weeks post injury that develops into strong spasticity after 2 months. Gene expression changes were studied in motor neurons 21 and 60 days after complete spinal transection where the tail exhibits clear signs of spasticity.
2009-11-01 | GSE16710 | GEO
Project description:To identify regulatory tissue regeneration enhancer elements (TREEs) relevant during spinal cord regeneration, we performed ATAC sequencing datasets of zebrafish spinal cord at 1 week after sham injury and after transection.
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