|
| Status |
Public on May 09, 2022 |
| Title |
mitfa:GFP+/crestin:mCherry+/double+ cells, CVT |
| Sample type |
SRA |
| |
|
| Source name |
mitfa:GFP+/crestin:mCherry+/double+ cells sorted from CVT-10216-treated 72hpf embryos 8 hours post MoTP washout
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tg(crestin:mCherry;mitfa:GFP)
developmental stage: 72hpf
treatment: MoTP+CVT-10216
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
scRNA-seq, paired end reads
library prepared with 10x genomics Chromium Single Cell 3’ Library Kit v3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
DMSO_CVT_combined.csv
DMSO_CVT_combined_filtered.csv
|
| Data processing |
Illumina software used for basecalling.
Reads from each library were aligned to the zebrafish genome (GRCz11) using the CellRanger pipeline (v.2.1.1)
Libraries were aggregated using the CellRanger pipeline (v.3.1.0, CellRanger aggregate)
The gene-cell aggregated matrix was subjected standard quality control with the Scater package (v.1.18.6). Only cells with total features >1000, log10 total counts > 3.0, and mitochondrial gene counts (%) < 20 were considered as high quality and kept
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: DMSO_CVT_combined.csv (Gene-cell aggregated matrix BEFORE filtering;comma separated (csv) file of raw counts at gene level for each cell)
Supplementary_files_format_and_content: DMSO_CVT_combined_filtered.csv (Gene-cell aggregated matrix AFTER filtering; comma separated (csv) file of raw counts at gene level for each cell)
Supplementary_files_format_and_content: The DMSO barcodes are followed with -1 and the CVT barcodes by -2.
|
| |
|
| Submission date |
Sep 10, 2021 |
| Last update date |
May 09, 2022 |
| Contact name |
Eleanor Elizabeth Patton |
| E-mail(s) |
e.patton@ed.ac.uk
|
| Organization name |
MRC Human Genetics Unit, Institute of Genes and Cancer, University of Edinburgh
|
| Street address |
MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road
|
| City |
Edinburgh |
| ZIP/Postal code |
eh42XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30614 |
| Series (1) |
| GSE183868 |
Aldh2 dependent formaldehyde metabolism fuels purine demands in melanocyte stem cells |
|
| Relations |
| BioSample |
SAMN21381062 |
| SRA |
SRX12149194 |
