|
| Status |
Public on Oct 01, 2021 |
| Title |
PSIAO |
| Sample type |
SRA |
| |
|
| Source name |
larval aboral tissue
|
| Organism |
Nematostella vectensis |
| Characteristics |
tissue: larval aboral tissue
developmental stage: planula
age: ~ 50-60 hours post fertilization
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Life technologies, USA) as instructed in manual.
RNA-seq libraries were constructed using SENSE mRNA-Seq Library Prep Kit (Lexogen GmbH). Each library was indexed in order to multiplex samples on the Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
A minimum of 20 million 2x150bp sequencing reads were collected from each sample. The data were pre-processed to remove the adapters using Trimmomatic v0.36
pre-processed reads were mapped to the Nematostella vectensis genome (indexed bowtie2) by using STAR.
The number of reads mapping to each Nematostella gene models was extracted using HTSeq-count v0.6
Differential expression analyses were performed using limma (Galaxy Version 2.11.40.6) and DESeq2 (Galaxy Version 2.11.40.6)
Genome_build: Nematostella vectensis (ASM20922v1)
Supplementary_files_format_and_content: tab-delimited text file includes read counts generated using HTSeq-count v0.6 tool (The NVE gene models are available at https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696)
|
| |
|
| Submission date |
Oct 07, 2020 |
| Last update date |
Oct 01, 2021 |
| Contact name |
vengamanaidu modepalli |
| E-mail(s) |
vengamanaidumodepalli@gmail.com
|
| Organization name |
Marine Biological Association of the UK
|
| Department |
Cell and Molecular
|
| Lab |
Dr Vengamanaidu Modepalli
|
| Street address |
The Laboratory,Citadel Hill
|
| City |
Plymouth, Devon |
| State/province |
--- |
| ZIP/Postal code |
PL1 2PB, |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL29226 |
| Series (1) |
| GSE159166 |
Spatial transcriptome of Nematostella vectensis apical organ reveals its molecular signature and associated cells |
|
| Relations |
| BioSample |
SAMN16387603 |
| SRA |
SRX9257240 |
