|
| Status |
Public on Sep 24, 2021 |
| Title |
scLv-3hpf |
| Sample type |
SRA |
| |
|
| Source name |
Single cells 3 hours post fertilization
|
| Organism |
Lytechinus variegatus |
| Characteristics |
embryonic stage: 16-cell stage
genotype: Wild Type - Collected at Beaufort, NC.
|
| Treatment protocol |
Fertilization of sea urchin embryos in 03.g PABA/100 mL artificial sea water.
|
| Growth protocol |
Sea urchin embryos stirred and cultured at 23˚C in artificial sea water
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hourly embryo dissociations using calcium-free artificial sea water, glycine, EDTA, methanol, and 3x SSC.
10x Genomics Single Cell 3' kit v3; Samples sequenced using two S1 flow cells with two lanes each (4 lanes total)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
10x Cell Ranger v3.0.1 software "mkfastq" function
10x Cell Ranger v3.0.1 software "count" function
10x Cell Ranger v3.0.1 software "aggr" function
Seurat v3.1 software standard workflow
Genome_build: Lytechinus variegatus genome assembly v 3.0
Supplementary_files_format_and_content: comma-separated value text files with UMI counts for each of the samples
Supplementary_files_format_and_content: Interactive 10x cloupe file with all samples aggregated, analyzed, and visualized
Supplementary_files_format_and_content: RDS file with all samples aggregated, analyzed, and visualized into 63 clusters using Seurat
|
| |
|
| Submission date |
Sep 21, 2021 |
| Last update date |
Sep 24, 2021 |
| Contact name |
David R McClay |
| Organization name |
Duke University
|
| Department |
Biology
|
| Street address |
124 Science Drive room 4115
|
| City |
Durham |
| ZIP/Postal code |
27707 |
| Country |
USA |
| |
|
| Platform ID |
GPL30656 |
| Series (1) |
| GSE184538 |
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo |
|
| Relations |
| BioSample |
SAMN21537589 |
| SRA |
SRX12285931 |
