|
| Status |
Public on Jan 08, 2015 |
| Title |
FLAG-CEY2_MYC_IP_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole-worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
time in development: young adults
strain: rrrSi233 [cey-2pro::FLAG(1x)::cey-2ORF::cey-2 3’-UTR::operon linker::PEST:GFPH2B::tbb-2 3'UTR; unc-119(+)] I
|
| Treatment protocol |
Worms were washed of the plates, washed three times with M9 and frozen in liquid nitrogen
|
| Growth protocol |
C. elegans eggs were allowed to hatch overnight, hatched L1s were plated on NG 2% plates seeded with OP50, grown to young adult stage and harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was dissociated from beads by adding Trizol Reagent (Life Technologies) directly to the beads, followed by the normal extraction protocol
Library preparation was performed using the ScriptSeq v2 RNA-Seq library preparation kit (Epicentre) according to the manufacturer's protocol
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The RNA-seq data (50bp read length) were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size of all MYC controls. The MYC controls were chosen as a reference for sequence depth because they had substantially fewer reads than the FLAG-IPs. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce6
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Oct 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dimos Gaidatzis |
| E-mail(s) |
d.gaidatzis@fmi.ch
|
| Organization name |
Friedrich Miescher Institute
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18245 |
| Series (2) |
| GSE62856 |
Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RIP-Seq) |
| GSE62861 |
Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes |
|
| Relations |
| BioSample |
SAMN03153509 |
| SRA |
SRX747672 |
