|
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 |