|
| Status |
Public on Jan 08, 2015 |
| Title |
RNASeq_N2_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole-worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
time in development: young adults
strain: N2
|
| 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 |
Total RNA isolation was performed using Trizol Reagent (Life Technologies). Important: Total RNA was extracted from the same lysate used subsequently for the corresponding ribosome profiling experiment.
Library preparation was performed using the ScriptSeq v2 RNA-Seq library preparation kit (Epicentre) according to the manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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, each library was normalized to a total of 22.3M reads which represents the smallest library size considering RNA-seq as well as matching RPF samples. 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) |
| GSE62858 |
Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RNA-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 |
SAMN03153516 |
| SRA |
SRX747687 |
