|
| Status |
Public on Apr 01, 2015 |
| Title |
rrf-3 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: rrf-3
developmental stage: adult
transgenes: wormcherry piRNA sensor
tissue: whole animal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions and followed by an overnight precipitation at -20C using isopropanol and glycogen as a carrier. For RIP, custom Anti HRDE-1 polyclonal antibody was generated by Genomic Antibody Technology(GAT) by SDIX (Newark USA) against amino acids 12-161 of HRDE-1.
Before library preparation, 1-5ug of total RNA was treated with 1ul of RNA polyphosphatase (Epicentre) for 30 minutes at 37C. RNA was then extracted using Phenol/chloroform and precipitated overnight at -20C using Ethanol and Sodium Acetate. Following this we followed the Illumina Truseq small RNA protocol according to the manufacturer's instructions
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
5' polyphosphatase treated
|
| Data processing |
Adapter trimming using the fastX toolkit fastx_collapser module
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed to give only unique sequence, along with read count for each, the using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: Fasta header: id_number of reads
|
| |
|
| Submission date |
Feb 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Sarkies |
| E-mail(s) |
[email protected]
|
| Organization name |
Imperial College London
|
| Department |
MRC Clinical Sciences Centre
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18730 |
| Series (1) |
| GSE66344 |
Small RNA sequencing of transgenes silencing by paramutation in C. elegans |
|
| Relations |
| BioSample |
SAMN03378749 |
| SRA |
SRX892599 |
