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| Status |
Public on Jun 07, 2023 |
| Title |
sc-RNAseq of the day 4 zebrafish spinal cord |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish. Electrophysiological studies have shown that additional to connectivity, understanding of circuitry requires identification of functional specializations among individual circuit components, such as those that regulate levels of transmitter release and neuronal excitability. In this study we use single cell RNAseq (scRNAseq) to identify molecular distinctions causal to the unique physiology of primary motoneuron (PMn) function, as well as associated specialized interneurons that are tailored specifically for mediation of the powerful escape response. Generating scRNA-seq datasets that provide both a wide overview of the cellular populations of the spinal cord and a granular view of the zebrafish motor neurons.
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| Overall design |
Cells from the spinal cords of 150 tg(SAIG213a;EGFP) zebrafish were analyzed via scRNA-seq and populations of interneurons were identified based on established markers. For examination of Motor neurons we additionally preformed FACS on cells dissociated from spinal cords of 150 tg(mnx1:GFP) zebrafish.
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| Contributor(s) |
Wen H, Brehm P, Kelly JJ |
| Citation(s) |
37333232, 37975797 |
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| Submission date |
May 18, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Paul Brehm |
| E-mail(s) |
brehmp@ohsu.edu
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| Organization name |
Oregon Health and Science University
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| Department |
Vollum
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| Lab |
Brehm
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| Street address |
3232 SW Research Drive
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA973994 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE232801_Integrated_spine.RDS.gz |
2.1 Gb |
(ftp)(http) |
RDS |
| GSE232801_Motor_Neuron.RDS.gz |
1.9 Gb |
(ftp)(http) |
RDS |
| GSE232801_Neurons.RDS.gz |
928.5 Mb |
(ftp)(http) |
RDS |
| GSE232801_RAW.tar |
173.9 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
| GSE232801_zebrafish_custom_reference.GTF.gz |
8.1 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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