|
| Status |
Public on Jan 16, 2021 |
| Title |
nkx3.2 mutant cartilage |
| Sample type |
SRA |
| |
|
| Source name |
cartilage
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tg(fli1a:EGFP)y1;Tg(sox10:DsRed)el10
genotype: nkx3.2 el802/el802
age: 22 days post fertilization
tissue: cartilage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller
Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using 3' Gene Expression v2 Library kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10X Genomics single cell barcoding
|
| Data processing |
Reads were aligned to z11 genome using Cell Ranger 3.
Genome_build: z11
Supplementary_files_format_and_content: barcode, gene and matrix files from Cell Ranger alignment and trimming
|
| |
|
| Submission date |
May 28, 2020 |
| Last update date |
Jan 16, 2021 |
| Contact name |
Joanna Smeeton |
| Organization name |
Columbia University Irving Medical Center
|
| Department |
Rehabilitation and Regenerative Medicine
|
| Lab |
Smeeton Lab
|
| Street address |
650 W 168TH ST, ROOM 1103A, William Black Building
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE151354 |
Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton |
|
| Relations |
| BioSample |
SAMN15044555 |
| SRA |
SRX8413198 |
