|
| Status |
Public on Apr 05, 2012 |
| Title |
Wild-type small RNAs Sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: Wild-type (N2)
developmental stage: mixed stage
tissue: Whole worm
|
| Growth protocol |
Worms were grown on OP50 lawn at 20 degrees Celsius
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolating using TRIzol reagent (Invitrogen), small RNAs were isolated by gel purication and cDNA was prepared using the small RNA v1.5 illumina kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
small RNA (18-30 nts) with 5' monophosphate
|
| Data processing |
Sequence reads were obtained using the Illumina Genome Analyzer Pipeline version 1.6 (OLB 1.6, CASAVA 1.6.0)
Alingment: Sequnces were aligned to the genome (May 2008) using Novoalign, with an r-value of 0.2 and a q-value of 5. Sequences were filtered using the USeq. software package component NovoalignParser, using a posterior probability of 0.1. Output is a bed file for each chromosome, with separate files for plus and minus strands.
|
| |
|
| Submission date |
Apr 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Bryan Warf |
| E-mail(s) |
warf@biochem.utah.edu
|
| Phone |
801-585-3110
|
| Organization name |
University of Utah
|
| Department |
Biochemistry
|
| Lab |
Brenda Bass
|
| Street address |
15 N Medical Dr East, room 4800
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE28888 |
Effects of ADARs on small RNA processing pathways in C. elegans |
|
| Relations |
| Reanalyzed by |
GSE89765 |
| SRA |
SRX059215 |
| BioSample |
SAMN00261233 |
