|
| Status |
Public on Apr 01, 2010 |
| Title |
dcr-1(-/-)K39A_1 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: BB93: dcr-1(ok247);uuEx18[dcr-1(K39A), dpy-30::mCherry]
stage: mixed
genotype/variation: dcr-1(ok247) animals expressing transgene containing Dicer with K39A mutation
|
| Growth protocol |
worm strains were grown on NGM agar plates at 20 C and mixed stage worms were isolated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from C. elegans strains using trizol. Total RNA (10 µg) was subjected to 5’ ligation-dependent library preparation (Illumina small RNA sequencing protocol V1.0). small RNAs were selected by gel purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
dcr-1(ok247) animals expressing transgene containing Dicer with K39A mutation
|
| Data processing |
Alignment: Reads were aligned to the May_2008 release of the C. elegans genome (ce6). Adapter sequences were trimmed and a gapped alignment was performed using the Novoalign software package (http://www.novocraft.com). In order to make these data useful for as many downstream users as possible, the provided novoalign .txt output files were created use a non-stringent posterior probability for alignment. These files should therefore be parsed based on the desired posterior probability before carrying out downstream analysis. The USeq software package contains one such parser and is available at: http://sourceforge.net/projects/useq/.
|
| |
|
| Submission date |
Feb 16, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Noah Welker |
| E-mail(s) |
nwelker@biochem.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Biochemistry
|
| Lab |
Brenda L. Bass
|
| Street address |
15 N Medical Drive E. Rm. 4800
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112-5650 |
| Country |
USA |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE20336 |
Comparison of small RNA levels in Dicer helicase mutants |
|
| Relations |
| SRA |
SRX016899 |
| BioSample |
SAMN00009021 |
