|
| Status |
Public on Oct 18, 2016 |
| Title |
rrr13_ets4RNAi_2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: rege-1(rrr13)
developmental stage: young adults
genotype: ets-4 knockdown
|
| Treatment protocol |
Synchronized L1 larvae were put on RNAi plates to facilitate knock down by feeding dsRNA directed against ets-4 or mock.
|
| Growth protocol |
Animals were synchronized by hypochloride treatment and allowed to hatch in M9 over night.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were grown to young adulthood, frozen in liquid nitrogen and RNA was extracted by Trizol treatment.
ScriptSeq v2 RNA-Seq Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ets-4i
|
| Data processing |
The RNA-seq data were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/3.1/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 (ce_mRNA_ets4RNAi_rawCounts.txt) was quantified by counting the number of reads that started within any of the exons belonging to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same") which counts the reads on the same strand as the gene. 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. 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 (ce_mRNA_ets4RNAi_normalized.txt).
Genome_build: ce6
Supplementary_files_format_and_content: ce_mRNA_ets4RNAi_rawCounts.txt and ce_mRNA_ets4RNAi_normalized.txt
|
| |
|
| Submission date |
Nov 18, 2015 |
| 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) |
| GSE75160 |
Whole RNA sequencing to identify targets of ets-4 that are responsible for rege-1 (C30F12.1) phenotype |
| GSE75163 |
Whole RNA sequencing to identify targets of ETS-4 and REGE-1 |
|
| Relations |
| BioSample |
SAMN04276983 |
| SRA |
SRX1437661 |
