|
| Status |
Public on Dec 09, 2011 |
| Title |
WHOLE_WORM_WILDTYPE |
| Sample type |
SRA |
| |
|
| Source name |
nematode whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype/variation: N2
cultivation temperture: 24°C
developmetal stage: young adult
|
| Growth protocol |
Worms were cultivated at 24°C on NGM plates as previously described (Stiernagle, 2006)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Illumina paired end polyA standard protocol (polyadenylated transcripts), fragment length ~250nt, insert size ~50nt.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
wildtype young adult
|
| Data processing |
Deep sequencing read libraries of WT and glp-4 samples were mapped to the C. elegans genome sequence (ws190) by running TOPHAT v1.3.1 (with parameters –i 30 –I 10000 --mate-inner-dist 250 --mate-std-dev 125) and using gene models (see manuscript) to provide reference splice junctions. Subsequently, isoform expression was quantified by running CUFFLINKS v1.0.3 60 using the same gene models as reference annotation. Expression of gene loci was estimated by summing up FPKM values of all isoforms and confidence intervals were determined by summing up lower and upper boundaries for isoform expression as determined by CUFFLINKS.
|
| |
|
| Submission date |
Nov 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Dominic Gruen |
| E-mail(s) |
dominic.gruen@mdc-berlin.de
|
| Organization name |
Max-Delbrueck-Center
|
| Street address |
Robert-Roessle-Strasse 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE33543 |
In vivo and transcriptome-wide identification of RNA-binding protein target sites |
| GSE33573 |
In vivo and transcriptome-wide identification of RNA-binding protein target sites [RNA-Seq] |
|
| Relations |
| SRA |
SRX105293 |
| BioSample |
SAMN00752519 |
