|
| Status |
Public on Apr 01, 2014 |
| Title |
prde-1_2 5' dependent |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: Young Adult
genotype/variation: prde-1 mutant
treatment: 5' polyphosphatase treated
tissue: whole animal
|
| Growth protocol |
Animals were synchronized at L1 stage using hypochlorite treatment, followed by growth to young adult stage on NGM/HB101 using standard procedures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trisure (BioLine) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-30nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: The .fasta files report seq_id_number of reads
|
| |
|
| Submission date |
Jul 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Sarkies |
| E-mail(s) |
psarkies@imperial.ac.uk
|
| 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 |
GPL15716 |
| Series (1) |
| GSE49220 |
Small RNA sequencing study of C elegans piRNA biogenesis factors |
|
| Relations |
| BioSample |
SAMN02265422 |
| SRA |
SRX328199 |
