|
| Status |
Public on Apr 07, 2012 |
| Title |
wild type pos-1 RNAi untreated |
| Sample type |
SRA |
| |
|
| Source name |
wild type adult animals, pos-1 RNAi, untreated
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: wild type
developmental stage: adult
RNAi: pos-1
rna treatment: none
|
| Treatment protocol |
For RNAi treatment, animals were dropped as L1 stage larvae on E. coli strain HT115 containing the indicated control or pos-1 RNAi plasmids and harvested as day one adults for RNA isolation.
|
| Growth protocol |
C. elegans were grown at 20˚C on E. coli strain OP50 or on strain HT115 containing RNAi plasmids.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from synchronized worms and small RNAs were size selected, either untreated or tobacco acid pyrophosphatase (TAP) treated to remove 5' di- and triphosphate groups, ligated to 5' and 3' adapters and subjected to reverse transcription and PCR. PCR amplicons were PAGE purified prior to sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 17.
~18-26 nt RNAs, untreated.
|
| Data processing |
Raw datasets are fastq files generated using Illumina software. The sequence of the 3' adapter used during library preparation is 5'-TGGAATTCTCGGGTGCCAAGG or 5'-CTGTAGGCACCATCAAT for samples 1-11 and samples 12-19, respectively. For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20. Sequences were not filtered for alignment to a genome. Unique sequences and corresponding read counts were generated using custom perl scripts.
Supplementary_files_format_and_content: Tab-delimited text file containing unique sequences and corresponding read counts.
|
| |
|
| Submission date |
Apr 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Taiowa Montgomery |
| E-mail(s) |
montgomery@molbio.mgh.harvard.edu
|
| Phone |
(617) 643-3319
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Molecular Biology
|
| Lab |
Ruvkun
|
| Street address |
185 Cambridge Street, CPZN-7250
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114-2790 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE37083 |
The Caenorhabditis elegans RDE-10/RDE-11 complex regulates RNAi by promoting secondary siRNA amplification |
|
| Relations |
| SRA |
SRX136704 |
| BioSample |
SAMN00849897 |
