|
Status |
Public on Apr 16, 2013 |
Title |
Nr22 Rotenone 10day rep1 |
Sample type |
SRA |
|
|
Source name |
total RNA from whole animals
|
Organism |
Caenorhabditis elegans |
Characteristics |
tissue: whole animal age: 10 days after L4 developmental stage: Adult (10 days after L4) treatment: 100nM rotenone
|
Treatment protocol |
Treatment of C. elegans was carried out on NGM agar plates containing respective complex I inhibitors. All agar plates were prepared from the same batch of NGM agar, whereas treatment plates were supplemented with the respective compound and control plates with the respective solvent
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at −80°C until use. Total RNA was inspected for degradation using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). For library preparation an amount of 2μg of total RNA per sample was processed using Illumina's TruSeq™ RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer's instruction. Each library includes its own index sequence.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
JA22
|
Data processing |
Illumina Casava1.7 software used for extraction of FASTQ files FASTQ files were mapped using TopHat (v1.4.1, parameters: --butterfly-search -g 1) vs. the C. elegans genome assembly WS220 (Ensembl release 66) Gene counts were obtained using the Python package HTSeq and the respective Ensembl annotation GTF file (parameters: –stranded=no --idattr=gene_id --mode=union) HTSeq result files were processed using the R programming language and RPKM values were calculated Genome_build: WS220 (ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.WS220.genomic.fa.gz)/WBcel235 Supplementary_files_format_and_content: raw counts and RPKM values for each sample
|
|
|
Submission date |
Apr 15, 2013 |
Last update date |
May 15, 2019 |
Contact name |
JenAge Project |
E-mail(s) |
geo-data@jenage.de
|
Organization name |
Leibniz Institute for Age Research - Fritz Lipmann Institute
|
Street address |
Beutenbergstr. 11
|
City |
Jena |
ZIP/Postal code |
D-07745 |
Country |
Germany |
|
|
Platform ID |
GPL13657 |
Series (1) |
GSE46051 |
Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence and absence of rotenone at 4 different time points |
|
Relations |
SRA |
SRX265369 |
BioSample |
SAMN02045786 |