|
| Status |
Public on Jan 01, 2019 |
| Title |
PIWI2_splice Morpholino_12 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Nematostella vectensis |
| Characteristics |
developmental stage: Early planula
treated: Morpholino
barcode: CTTGTA
|
| Treatment protocol |
The eggs were injected with Morpholino Antisense Oligonucleotide. The RNA periodate is carried out as follow, half of each sample was oxidized (5X borate buffer, ph=8.6; 5 μL freshly prepared 50mM sodium periodate) for 30 minutes at 25 degrees C, then precipitated with sodium acetate, ethanol and glycogen; the other half was not treated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Life technologies, USA) as instructed in manual, the small (18-30 nt long) RNA were purified on a denaturing 15% acrylamide gel, from 20 μg total RNA per sample. RNAs were eluted from the acrylamide bands overnight in 0.3 M NaCl, then ethanol/glycogen-precipitated.
Small RNA libraries were constructed as described in Phillip Zamore Lab Illumina TruSeq Small RNA Cloning Protocol April, 2014 (http://www.umassmed.edu/zamore/resources/protocols/). Each library was indexed in order to multiplex 30 samples per sequencing run on the Illumina.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
A minimum of 13 -15 million 50bp sequencing reads were collected from each sample.
The data were pre-processed to remove the adapters using cutadapt
pre-processed reads were analysed using miRDeep2 software (https://www.mdc-berlin.de/8551903/en/)
Supplementary_files_format_and_content: counts of small RNA sequences
|
| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
vengamanaidu modepalli |
| E-mail(s) |
[email protected]
|
| 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 |
GPL23029 |
| Series (1) |
| GSE115184 |
The methyltransferase HEN1 is required for microRNA and piRNA stability as well as larval metamorphosis in Nematostella vectensis |
|
| Relations |
| BioSample |
SAMN09290422 |
| SRA |
SRX4149324 |
