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| Status |
Public on Sep 09, 2022 |
| Title |
planula2d |
| Sample type |
SRA |
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| Source name |
Early planula 2dpf
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| Organism |
Nematostella vectensis |
| Characteristics |
sample type: Early planula
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| Extracted molecule |
total RNA |
| Extraction protocol |
Whole embryos, animals, or dissected tissues were treated with TrypLETM Select Enzyme (A1217702, Thermo Fisher Scientific). Enzyme concentration and incubation time were adapted to each stage. Cell viability and counts were assayed with a Cellometer X2 (Nexcelom). Cell suspensions were diluted and loaded into a 10x Genomics single cell platform using vs2 and vs3 reagents.
10X Genomics Chromium v2/v3 chemistry
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
cellranger pipeline using default parameters with forced recovery of 7000 cells for each library
cells filtered for minimum 250 (vs2) or 350 (vs3) detected genes
library names were appended to barcodes from individual libraries
count matrices were concatenated into a single dataset
Assembly: Reads were mapped to the JGI genome assembly (Vs1) using a customized transcriptome (David Fredman 2013), wherein all gene models were extended by 1000bp in the 3’ direction, or until the start of the next gene model in the same orientation.
Supplementary files format and content: alldata.mtx: count matrix after demultiplexing, mapping, and UMI reduction for all libraries
Supplementary files format and content: alldata.genes.csv text file with gene names (NVE models: rows)
Supplementary files format and content: alldata.cells.csv text file with sample names (columns)
Supplementary files format and content: NVEmodels.gtf mapping coordinates for genome mapping
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| Submission date |
Apr 05, 2022 |
| Last update date |
Sep 09, 2022 |
| Contact name |
Alison G Cole |
| Organization name |
University of Vienna
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| Department |
Neurosciences and Developmental Biology
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| Street address |
Djerassiplatz 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL23029 |
| Series (1) |
| GSE200198 |
A time course of sea anemone development |
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| Relations |
| BioSample |
SAMN27350026 |
| SRA |
SRX14746742 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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