|
| Status |
Public on May 03, 2016 |
| Title |
lin-65(n3441) EV replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
lin-65(n3441) EV_whole worm lysate
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/line background: lin-65(n3441)
developmental stage: L4
RNAi treatment: empty vector (EV)
tissue: whole worm lysate
|
| Treatment protocol |
Animals were collected by washing with M9 at the L4 stage.
|
| Growth protocol |
N2, lin-65(n3441) and met-2(ok2307) animals were grown from hatch at 20C on either empty vector (EV) or EV+cco-1 RNAi bacteria.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Collected worms were snap frozen in liquid nitrogen. Pellets were grinded with a mortar and pestle on dry ice and the resulting powder was thawed in the presence of lysis buffer (50mM Tris-HCl, 50mM NaCl, 10mM MgCl2, 5mM CaCl2 200μg/ml cycloheximide, 200μg/ml heparin, 1% Triton X-100, 0.1% NaDOC) and incubated on ice for 10 minutes prior to centrifugation at 4C, 16,000 x g for 10 minutes. Total RNA was purified from clarified lysate using Trizol-LS (Life Technologies) and poly-A RNA was extracted with oligo-dT(25) Dynabeads (Ambion), each according to manufacturer’s instructions.
Sequencing libraries were prepared using the Epicentre ScriptSeq v2 according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina HiSeq 2500 reads were trimmed of adapter sequences and filtered for read that passed quality filtering
Reads were mapped to a set of C. elegans noncoding RNAs
Remaining reads were mapped to an index containing the longest single isoform ± 30nt for each gene in the C. elegans WS230 genome using Bowtie version 0.12.7 (Langmead et al., 2009) with the following settings: -m 1 -v 2 -a --norc --best --strata
In-house python scripts were used to count reads mapping to each transcript.
Tab-delimited .txt files include raw counts associated with each transcript and can be used as input for DESeq, where we used a standard pipeline to determine differential expression by padj < 0.05
Genome_build: Wormbase WS230
Supplementary_files_format_and_content: Tab-delimited .txt files include raw counts associated with each transcript
|
| |
|
| Submission date |
Feb 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Dillin |
| E-mail(s) |
dillin@berkeley.edu
|
| Organization name |
University of California, Berkeley
|
| Lab |
Dillin Lab, 430E Li Ka Shing
|
| Street address |
188 Li Ka Shing
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE78252 |
Mitochondrial stress induces chromatin reorganization to promote longevity and UPRmt |
|
| Relations |
| BioSample |
SAMN04513412 |
| SRA |
SRX1598270 |
