|
| Status |
Public on Jan 12, 2024 |
| Title |
2day_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
50-100 whole embryos
|
| Organism |
Nematostella vectensis |
| Characteristics |
tissue: 50-100 whole embryos
genotype: wildtype
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole embryos or dissected tissues were dissociated with collagenase (24hr_rep4 and mesentery_male) or tripleE (2day_rep2, interparietal bodywall). Mechanical force was used to disrupt the tissues and obtain single-cell suspensions. Cell suspensions were washed with 0.1% BSA (bovine serum albumin), and cell viability and counts were assayed with a Cellometer X2 (Nexcelom). Cell suspensions were diluted to 1000 cells/ microliter and loaded into a 10x Genomics single cell platform using vs3 reagents.
10X Genomics Chromium v2/v3 chemistry according to manufacturer protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
cellranger pipeline using default parameters with forced recovery of 10000 cells for each library
Assembly: PRJNA667495 from Zimmerman et al 2023 doi:10.1038/s41467-023-44080-7
Supplementary files format and content: extracted barcodes representing captured cells: XX_barcodes
Supplementary files format and content: gene designation: XX_features
Supplementary files format and content: extracted count matrix: XX_matrix
|
| |
|
| Submission date |
Jan 11, 2024 |
| Last update date |
Jan 12, 2024 |
| Contact name |
Alison G Cole |
| Organization name |
University of Vienna
|
| Department |
Neurosciences and Developmental Biology
|
| Street address |
Djerassiplatz 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL29226 |
| Series (1) |
| GSE200198 |
A time course of sea anemone development |
|
| Relations |
| BioSample |
SAMN39408961 |
| SRA |
SRX23168417 |
