|
| Status |
Public on Apr 02, 2024 |
| Title |
glia, AB42 |
| Sample type |
SRA |
| |
|
| Source name |
telencephalon
|
| Organism |
Danio rerio |
| Characteristics |
tissue: telencephalon
genotype: Tg(fli1a:GFP)
treatment: AB42
|
| Treatment protocol |
Tg(her4.1:dRED) and Tg(fli1a:GFP) lines were injected with Amyloid-beta 42 peptide and PBS as control as descibed (Bhatatrai et al. 2016).
|
| Growth protocol |
Zebrafish were kept in the re-circulating system on a 14/10-h light/dark cycle, pH 7.5, at 28 °C (±1 °C) in groups of 20 animals per 2.8 L.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from zebrafish telencephalon were dissociated, cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol.
10X genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10x Genomics
CP015
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger
|
| |
|
| Submission date |
Feb 21, 2023 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Caghan Kizil |
| E-mail(s) |
ck2893@cumc.columbia.edu
|
| Phone |
4752570197
|
| 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 |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE225721 |
Single cell transcriptomics on zebrafish gliovascular niche |
|
| Relations |
| BioSample |
SAMN33396051 |
| SRA |
SRX19457377 |
