|
| Status |
Public on Nov 01, 2021 |
| Title |
FACS sorted NC cells 24 hpf |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted sox10:nEOS cells
|
| Organism |
Danio rerio |
| Characteristics |
genotype: Tg(sox10:nEOS)w18
age: 24 hpf
cell type: NC cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II.
Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7, which used chemistry v3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
aggregated.arch.counts.matrix.csv
Sample 5
|
| Data processing |
FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger.
Further processing was performed using Seurat v3 in R
Low quality cells and doublets were excluded based on thresholds for number of genes detected (>1500; <4000)
Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected (<4%)
Genome_build: GRCz11
Supplementary_files_format_and_content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds. In aggregated.arch.counts.matrix.csv, barcode.1 corresponds to "Sample 1", barcode.2 corresponds to "Sample 2", and so on.
|
| |
|
| Submission date |
Mar 03, 2021 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Thomas F Schilling |
| E-mail(s) |
tschilli@uci.edu
|
| Phone |
(949) 824-7203
|
| Organization name |
University of California Irvine
|
| Department |
Developmental and Cell Biology
|
| Lab |
Thomas F. Schilling
|
| Street address |
4462 Natural Sciences II
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE168133 |
scRNA-seq timeline of first pharyngeal arch migratory stream in zebrafish |
| GSE168179 |
A single-cell transcriptomic analysis of cranial neural crest development reveals timing of lineage decisions and novel regulators |
|
| Relations |
| BioSample |
SAMN18121427 |
| SRA |
SRX10218347 |
