|
| Status |
Public on Oct 21, 2024 |
| Title |
tomo_Polyp14_48hpa |
| Sample type |
SRA |
| |
|
| Source name |
tomo-seq slices
|
| Organism |
Nematostella vectensis |
| Characteristics |
tissue: tomo-seq slices
developmental stage: unfed polyp, 3 week old
treatment: 48 hpa
|
| Treatment protocol |
amputation of the aboral tip
|
| Growth protocol |
3 week old unfed polyps were used
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
cDNA from tissue slices was generated using CEL-seq2 (Hashimshony et al. 2016). Experiments were performed by Single Cell Discoveries.
Illumina TruSeq small RNA sample preperation was performed by Single Cell Discoveries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
b3-MKK-4
|
| Data processing |
Sequencing reads were mapped against the Nematostella transcriptome (Zimmermann et al. 2022) using kallisto.
Kallisto | bustools (Melsted & Booeshaghi et al. 2021) was also used to count UMIs and to generate slice/gene matrices per sample.
Assembly: Nematostella transcripome Nvec200 (Zimmermann et al. 2022)
Supplementary files format and content: tomo_stella_allSlices.RDS, Seurat object containing all final slices including meta data information across all time points.
Supplementary files format and content: tomo_stella_intactSlices.RDS, Seurat object containing all final slices including meta data information for intact polyps only.
|
| |
|
| Submission date |
Jul 05, 2024 |
| Last update date |
Oct 21, 2024 |
| Contact name |
Tobias Gerber |
| E-mail(s) |
tobias.gerber@embl.de
|
| Organization name |
EMBL Heidelberg
|
| Department |
Developmental Biology
|
| Lab |
Detlev Arendt
|
| Street address |
Meyerhofstr. 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL34680 |
| Series (1) |
| GSE271567 |
Systemic coordination of whole-body tissue remodeling during local regeneration in sea anemones |
|
| Relations |
| BioSample |
SAMN40074208 |
| SRA |
SRX23715027 |
