|
| Status |
Public on Feb 25, 2010 |
| Title |
WT_TAP_seq_prb_s5 |
| Sample type |
SRA |
| |
|
| Source name |
gravid adult worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: Wild type N2
developmental stage: adult
|
| Treatment protocol |
n/a
|
| Growth protocol |
Animals were grown at 20 C for approximately 60-70h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA amplicons were prepared as described in Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline. Mol Cell. , 2009 Oct 2 [PMID: 19800275]
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
TAP cloning method, as described in Distinct Argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline [of the biogenesis and diversity of 22G-RNAs and suggest additional regulatory functions for small RNAs [PMID: 19800275].
|
| Data processing |
Small RNA sequences longer than 17 nt were mapped to the Caenorhabditis elegans genome (WS192, www.wormbase.org). Sequences that matched tRNA or rRNA sequences were then removed. Only full-length perfect matches were allowed. siRNA-targeted loci were defined as a region containing at least 25 reads per million matching reads. Relative abundance at each locus was determined by calculating (22G-RNAs in mutant(or)IP)/(22G-RNAs in wt+22G-RNAs in mutant(or)IP ).
|
| |
|
| Submission date |
Oct 23, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig Mello |
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Craig Mello
|
| Street address |
368 Plantatoin Street, Suite AS5-2047
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE18714 |
Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in ERGO-1/Argonaute pathway |
|
| Relations |
| SRA |
SRX017047 |
| BioSample |
SAMN00009259 |
