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Status |
Public on Sep 09, 2022 |
Title |
Nematostella vectensis Sub-adult bodywall single cell RNA sequencing run 1 |
Sample type |
SRA |
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Source name |
Sub-adult bodywall
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Organism |
Nematostella vectensis |
Characteristics |
tissue: bodywall
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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 |
SAMN15493430 |
SRA |
SRX8699981 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4663946_BodywallBarcodes.tsv.gz |
27.6 Kb |
(ftp)(http) |
TSV |
GSM4663946_BodywallMatrix.mtx.gz |
4.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data provided as supplementary file |
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