|
| Status |
Public on Jun 22, 2012 |
| Title |
N2 mex-3 RNAi |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
RNAi: mex-3
tissue: embryo
|
| Treatment protocol |
Whole embryos were fixed in Trizol 400 minutes following adult bleaching.
|
| Growth protocol |
Worms were grown on NGM-special plates at 25ËC and fed RNAi expressing bacteria.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fixed animals were freeze-cracked, lysed, and the lysate purified. mRNA's were polyA selected. Libraries were constructed and sequenced as per Illumina's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
cDNA from mRNA
RNA-seq
|
| Data processing |
Alignment: Sequence reads were obtained and aligned to the C. elegans genome using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml)
Peaks: Shifted peaks were identified using the software package Erange (http://woldlab.caltech.edu/rnaseq)
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Diane E Trout |
| Organization name |
California Institute of Technology
|
| Department |
Biology
|
| Lab |
Wold
|
| Street address |
1200 E California Blvd M/C 156-29
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL9309 |
| Series (2) |
| GSE28562 |
Genome-wide RNA expression in muscle-enriched embryos across different mutations. |
| GSE28563 |
HLH-1 binding in muscle-enriched embryos and RNA expression in muscle-enriched embryos across different mutations |
|
| Relations |
| BioSample |
SAMN02198563 |
