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| Status |
Public on Sep 09, 2022 |
| Title |
Nematostella vectensis Sub-adult pharynx single cell RNA sequencing run 1 |
| Sample type |
SRA |
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| Source name |
Sub-adult pharynx
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| Organism |
Nematostella vectensis |
| Characteristics |
tissue: phaynx
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| Extracted molecule |
total RNA |
| Extraction protocol |
5-month old Nematostella vectensispolyps were dissected into 4 separate tissues: tentacles, mesenteries, pharynx, bodywall. Tissue pieces were treated with undiluted TrypLETM Select (Thermo Fisher, A1217701). For 1 hour the tissues were allowed to disintegrate in the enzyme with gentle agitation on a shaker, then dissociation into single-cell suspensions was completed with occasional pipetting over the course of another 1.5 hrs. Cell viability and counts were assayed with a Cellometer X2 (Nexcelom), and suspensions were diluted to 1000 – 1700 cells/uL and loaded into a 10x Genomics single cell platform using Vs.2 reagents.
10X Genomics Chromium v2 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 2.1.0 pipeline using default parameters with forced recovery of 7000 cells for each library
The sequences for all NVE gene models are publicly available here:
https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
with the exception that the gtf file of transcript coordinates was modified
by extending all gene models 1000bp in the 3' direction or until
Genome_build: intersecting the next gene model in the same orientation, whichever
Supplementary_files_format_and_content: occurred first.
Supplementary_files_format_and_content: Barcodes.tsv = column names (cell index)
Supplementary_files_format_and_content: genes.tsv = row names (genes)
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| Submission date |
Jul 09, 2020 |
| 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 (2) |
| GSE154105 |
Sea anemone single cell tissue profiling [scRNA-seq] |
| GSE154477 |
Transcriptomic profiling of sea anemone tissues |
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| Relations |
| BioSample |
SAMN15493431 |
| SRA |
SRX8699980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4663945_PharynxBarcodes.tsv.gz |
27.6 Kb |
(ftp)(http) |
TSV |
| GSM4663945_PharynxMatrix.mtx.gz |
5.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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