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| Status |
Public on Aug 15, 2017 |
| Title |
Blastula 3, oxidized |
| Sample type |
SRA |
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| Source name |
whole animal
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| Organism |
Nematostella vectensis |
| Characteristics |
tissue: whole animal
developmental stage: Blastula
treatment: RNA Periodate
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| Treatment protocol |
Half of each sample was treated with periodate (oxidized).
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| 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. 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.
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.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Barcode: GCCAAT
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| 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/)
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| Submission date |
Feb 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
vengamanaidu modepalli |
| E-mail(s) |
[email protected]
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| Organization name |
Marine Biological Association of the UK
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| Department |
Cell and Molecular
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| Lab |
Dr Vengamanaidu Modepalli
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| Street address |
The Laboratory,Citadel Hill
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| City |
Plymouth, Devon |
| State/province |
--- |
| ZIP/Postal code |
PL1 2PB, |
| Country |
United Kingdom |
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| Platform ID |
GPL23029 |
| Series (1) |
| GSE94526 |
Post transcriptional modifications of miRNAs in the cnidarian Nematostella vectensis |
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| Relations |
| BioSample |
SAMN06298865 |
| SRA |
SRX2538826 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2477593_4_Blastula2_untreated.collapse_reads.txt.gz |
31.9 Mb |
(ftp)(http) |
TXT |
| GSM2477593_4_Blastula2_untreated.txt.gz |
1.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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