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Sample GSM1325242 Query DataSets for GSM1325242
Status Public on Mar 07, 2014
Title Nr36 +GlcN
Sample type SRA
 
Source name total RNA from liver
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: 108 weeks of age
agent: 10 g / kg GlcN in Diet
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.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Nr36
Data processing Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v1.4.1); C. elegans samples were mapped vs. the C. elegans genome (ce10); M. musculus samples were mapped vs. the M. musculus genome (mm10)
For counting the reads per gene (raw counts) the Python package HTSeq was used in mode ‘union’ together with the Ensembl gene annotation. Only uniquely mapable reads were regarded.
Genome_build: ce10
Genome_build: mm10
Supplementary_files_format_and_content: Nr01-12_25-36_counts_ce_mm.xls
 
Submission date Feb 10, 2014
Last update date May 15, 2019
Contact name Marco Groth
E-mail(s) cfngs@leibniz-fli.de
Organization name Leibniz Institute on Aging - FLI
Department Core Facility - Next Generation Sequencing
Street address Beutenbergstraße 11
City Jena
ZIP/Postal code 07747
Country Germany
 
Platform ID GPL13112
Series (1)
GSE54853 RNA-seq of C.elegans and M.musculus in the presence and absence of D-Glucosamine (GlcN)
Relations
BioSample SAMN02639721
SRA SRX469133

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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