|
| Status |
Public on Dec 10, 2011 |
| Title |
wild type, 52 h, beta eliminated |
| Sample type |
SRA |
| |
|
| Source name |
Whole worms, larvae, beta eliminated
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype: wild type
tissue: whole body
developmental stage: L4 larvae
treatment: beta elimination
|
| Growth protocol |
Animals were grown at 20˚C on E. coli strain OP50.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from synchronized animals, and small RNAs were size selected, either treated with sodium periodate followed by beta elimination or untreated, tobacco acid pyrophosphatase (TAP)-treated to remove 5' di- and triphosphate groups, ligated to 3' and 5' adapters and subjected to RT-PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Small RNA
|
| Data processing |
Raw datasets are fastq files generated using Illumina software. The sequence of the 3' adapter used during library preparation is 5'-TGGAATTCTCGGGTGCCAAGG. 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. Tab-delimited files containing unique sequences and corresponding read counts were generated using custom Perl scripts.
|
| |
|
| Submission date |
Dec 09, 2011 |
| 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 (2) |
| GSE34321 |
Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans |
| GSE35550 |
Analysis of 22G siRNA triggered siRNA amplification and 3' 2'-O-methylated small RNAs in Caenorhabditis elegans |
|
| Relations |
| SRA |
SRX111401 |
| BioSample |
SAMN00765492 |
