|
| Status |
Public on Jan 17, 2024 |
| Title |
AMI_AO_I |
| Sample type |
SRA |
| |
|
| Source name |
larval aboral tissue
|
| Organism |
Acropora millepora |
| Characteristics |
tissue: larval aboral tissue
developmental stage: planula
genotype: wild type (WT)
|
| Treatment protocol |
To separate the apical region from the rest of the larval body, we performed microdissection on Nematostella, Aurelia aurita, Acropora millepora and Acropora tenuis larvae as described in our previous study in Nematostella. Apical tissue containing the apical organ was isolated using 34 gauge needles under a stereomicroscope with 10X magnification. Motile larvae were placed into a fresh plastic Petri dish filled with Nematostella medium or filtered seawater. The larvae tend to adhere briefly to the bottom of a new plastic Petri dish, allowing enough time to separate the apical tissue by cutting. Each sample was pooled from a minimum of 100 individual larvae. For each planula prior to dissection, the frontal region is identified by means of the direction of larvae swimming. The samples were carefully collected using glass Pasteur pipettes, the excess medium was removed, and the samples were snap-frozen in liquid nitrogen and stored at -80°C until further processing.
|
| Growth protocol |
Nematostella: Polyps were grown in 16 ‰ artificial seawater at 18°C in the dark and fed with freshly hatched Artemia nauplii. Aurelia aurita: Ephyras were collected using a plankton net in the vicinity of Plymouth Sound, UK and cultured in seawater at 18°C in a 12:12 light and dark cycle. The jellyfish were fed twice a day with freshly hatched Artemia nauplii. Acropora millepora and Acropora tenuis: The corals were cultured in ex-situ. During the annual spawning, the embryos were collected after fertilisation. The larvae are maintained in artificial seawater and collected for experimentation at the planula stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, due to the sheer size, samples collected from multiple batches were combined to acquire an adequate amount of RNA for sequencing. Total RNA was isolated using the TRI Reagent® according to the manufacturer’s protocol. RNA quality was assessed using Agilent RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer (Agilent, USA), and samples with RNA integrity number ≥ 8.0 were used for sequencing.
The CORALL RNA-Seq Library Prep Kit (Lexogen GmbH) was used for library preparation. Before sequencing, the libraries were pre-assessed by Agilent High Sensitivity DNA Kit (Agilent, USA) and quantified using Qubit™ 1X dsDNA HS Assay Kit (Invitrogen™).
The sequencing was outsourced (GENEWIZ Illumina NovaSeq™ 2x150 bp sequencing), generating 15 million paired-end reads per replicate.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The De-multiplexing fastQ files were filtering high-quality sequencing reads, and the adapter contamination was removed using fastp an ultra-fast all-in-one FASTQ preprocessor
The quality of the reads was verified using FastQC
Processed reads from each sample were mapped to the respective genome and gene models (indexed bowtie2) by using STAR
The number of reads mapping to the respective gene model were extracted from STAR output using the featureCounts tool
Assembly: Nematostella vectensis (ASM20922v1); Aurelia aurita (GCA_004194395.1); Acropora tenuis ( GCA_014633955.1); Acropora millepora (GCF_013753865.1)
Supplementary files format and content: Tab-delimited text files include read counts
|
| |
|
| Submission date |
Sep 01, 2023 |
| Last update date |
Jan 17, 2024 |
| 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 |
GPL33727 |
| Series (1) |
| GSE242174 |
Reconstructing the gene regulatory network that shaped the evolution of larval sensory structure with a long ciliary tuft in Cnidaria. |
|
| Relations |
| BioSample |
SAMN37232825 |
| SRA |
SRX21592632 |
