|
| Status |
Public on Jul 31, 2020 |
| Title |
48 hours post fertilization embryos |
| Sample type |
SRA |
| |
|
| Source name |
48 hours post fertilization
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
time: 48 hours post fertilization
tissue: embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v3 chemistry and cells were loaded on a 10x Chromium Controller (10× Genomics, Pleasanton, CA). Libraries were sequenced on Illumina HiSeq with the configuration of 2x150 bp paired-end runs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
single cell mRNA
|
| Data processing |
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform single cells demultiplexing and UMI counting.The custom transcriptome reference was generated from assembly Spur_4.2 using CellRanger. Cells that have at least 400 or at most 2,500 genes detected were included in the downstream analysis using Seurat 3.1.4. The union of the top 2,000 highest dispersion genes from the compared datasets were selected for the alignment. T‐SNE projection and clustering analysis (dims = 1:15 and resolution = 0.5) were performed using Seurat. Markers were found using FindConservedMarkers and FindMarkers functions.
Genome_build: Spur_4.2
Supplementary_files_format_and_content: Seurat Object (RDS), Cell Ranger output files
|
| |
|
| Submission date |
Jul 30, 2020 |
| Last update date |
Jul 31, 2020 |
| Contact name |
nathalie oulhen |
| E-mail(s) |
[email protected]
|
| Organization name |
Brown university
|
| Street address |
185 meeting street
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02912 |
| Country |
USA |
| |
|
| Platform ID |
GPL28450 |
| Series (1) |
| GSE155427 |
Regulation of dynamic pigment cell states at single-cell resolution |
|
| Relations |
| BioSample |
SAMN15677803 |
| SRA |
SRX8853396 |
