|
| Status |
Public on Jul 30, 2021 |
| Title |
ExoRNA11250Hy |
| Sample type |
SRA |
| |
|
| Source name |
Extracellular vescicle
|
| Organism |
Hydra vulgaris |
| Characteristics |
strain: Zurich
|
| Treatment protocol |
Prior to total RNA extraction, EVs isolated by ultracentrifugation were enzymatically treated to eliminate the free RNA derived from the ribonucleoprotein complexes. Isolated vesicles were treated with 1 mg/mL of proteinase K for 30 min at 37°C, incubated 10 min at 65°C to inactivate the proteinase K and then treated with 10 µg/mL of RNAse A for 15 min at 37°C.
|
| Growth protocol |
For EV collection, 250 polyps were placed in 10 mL of Hydra solution in 6 cm Petri dishes and starved 4 days before processing for RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed on EV samples using “Total RNA Purification Kit” (Norgen Biotek Corp.) and following the manufacturer’s supplementary protocol for exosomal RNA purification, with one modification: the optional DNA removal step was carried out using RQ1 RNase-Free DNAse (Promega) at 0.1 U/mL.
Libraries were prepared with the Ovation SoLo RNA-seq system (NuGEN Technologies) according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were cleaned to remove the first 5 bases of read1, the Illumina adapter sequence 'AGATCGGAAGAGC' and with quality threshold 20 and minimum sequence length 35 using the program TrimGalore!
Pseudoalignment and gene expression quantification was performed with kallisto directly on transcript sequences
Genome_build: GCF_000004095.1_Hydra_RP_1.0_rna
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Jul 27, 2021 |
| Last update date |
Jul 30, 2021 |
| Contact name |
Claudia Tortiglione |
| E-mail(s) |
claudia.tortiglione@cnr.it
|
| Organization name |
National Research Council of Italy
|
| Department |
Istituto di Scienze Applicate e Sistemi Intelligenti "E.caianiello"
|
| Lab |
Nanobiomolecular group
|
| Street address |
Via Campi Flegrei, 34
|
| City |
Pozzuoli |
| ZIP/Postal code |
80078 |
| Country |
Italy |
| |
|
| Platform ID |
GPL28733 |
| Series (1) |
| GSE180886 |
Extracellular vesicles mediate molecular signalling during Hydra regeneration |
|
| Relations |
| BioSample |
SAMN20426910 |
| SRA |
SRX11561842 |
