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Sample GSM3523439 Query DataSets for GSM3523439
Status Public on Jan 01, 2019
Title Starv15h1
Sample type SRA
 
Source name whole organism
Organism Caenorhabditis elegans
Characteristics strain: wildtype (N2)
treatment: 15h starvation
tissue: whole organism
Treatment protocol Synchronized L4 worms were placed on stress plates (200uM fluphenazine, 200uM cantharidin, 10uM bortezomib or 25uM bortezomib) and collected the next day. For rpn-6 RNAi treatment, synchronized L3 worms were placed on RNAi plates and collected at day 1. For starvation, synchronized worms were placed on empty plates 15h prior collection. Control worms were not treated.
Growth protocol Synchronized worms were grown on 20°C until day 1 of adulthood. Food source: E. coli OP50
Extracted molecule total RNA
Extraction protocol The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen). RNA was subsequently purified using the RNeasy kit (Qiagen).
Illumina RNASeq library Protocol
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline
Sequenced reads mapped to C elegans
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: caenorhabditis_elegans
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each Sample
 
Submission date Dec 20, 2018
Last update date Jan 01, 2019
Contact name Thorsten Hoppe
E-mail(s) thorsten.hoppe@uni-koeln.de
Organization name CECAD Cologne and Institute for Genetics
Department Institut für Genetik
Lab Hoppe Lab
Street address Joseph-Stelzmann-Str. 26
City Cologne
ZIP/Postal code 50931
Country Germany
 
Platform ID GPL13776
Series (1)
GSE124178 RNA-seq: WT under proteotoxic stress conditions
Relations
BioSample SAMN10620080
SRA SRX5169886

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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