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| Status |
Public on Apr 02, 2024 |
| Title |
Single cell transcriptomics on zebrafish gliovascular niche |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To investigate the cell types involved in the gliovascular niche of the zebrafish brain, we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.
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| Overall design |
Tg(her4.1:dRED) and Tg(fli1a:GFP) lines were injected with Amyloid-beta 42 peptide as descibed (Bhatatrai et al. 2016) and cells were dissociated sorted by FACS as described (Cosacak et al. 2019). The single-cell encapsulation, cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom (GRChZ 11) and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit, and Sequencing done by Illumina.
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| Contributor(s) |
Bhattarai P, Cosacak MI, Yilmaz E, Kizil C |
| Citation(s) |
38260431, 38598053, 38902234 |
| |
| Submission date |
Feb 21, 2023 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Caghan Kizil |
| E-mail(s) |
ck2893@cumc.columbia.edu
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| Phone |
4752570197
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| Organization name |
Columbia University Irving Medical Center
|
| Street address |
650 W 168th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA937226 |
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