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Sample GSM1128872 Query DataSets for GSM1128872
Status Public on Nov 06, 2013
Title Nr33 DOG 20day rep2
Sample type SRA
 
Source name total RNA from whole animals
Organism Caenorhabditis elegans
Characteristics developmental stage: Adult (20 days after L4)
age: 20 days after L4
strain: N2 (var. Bristol)
agent: 5mM DOG
Treatment protocol Treatment of C. elegans was carried out on NGM agar plates containing 5 mM Of 2-deoxy-D-glucose. All agar plates were prepared from the same batch of NGM agar, whereas treatment plates were supplemented with the respective compound.
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 JA33
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)
Supplementary_files_format_and_content: raw counts and RPKM values for each sample
 
Submission date Apr 24, 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)
GSE46344 Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence of 2-deoxy-D-glucose (DOG) at 4 different time points
Relations
BioSample SAMN02056006
SRA SRX271498

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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