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Sample GSM1278056 Query DataSets for GSM1278056
Status Public on Apr 15, 2014
Title rat RNAseq data 10
Sample type SRA
 
Source name liver
Organism Rattus norvegicus
Characteristics tissue: liver
Sex: male
individuals: individual 1
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Strand‐specific (marmoset) and non-strand-specific (elephant) RNA-seq libraries were prepared according to the Directional mRNA‐seq Library Prep Pre‐Release Protocols from Illumina for male and female heart, liver, kidney, frontal cortex, cerebellum, ovary and testis (marmoset), and fibroblast (elephant). The testis samples for the common marmoset come from two different individuals. Marmoset tissues were obtained from the German Primate Center ("Deutsches Primatenzentrum") in Göttingen, Germany. Elephant fibroblasts were obtained from the Australian National University, Canberra, Australia. Each of these libraries were sequenced (101 cycles, single‐end) using the Illumina HiSeq 2000 platform, except for marmoset testis samples (individual 2) and both elephant fibroblast samples that were sequenced (79 cycles, single‐end) using the Illumina Illumina Genome Analyzer IIx platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description polyadenylated RNA fraction
rat_normalized_all_tissues_FPKM.txt
Data processing All RNA-seq reads were mapped with TopHat 1.4.0
Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) was then used to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations
Expression levels were normalized across samples and species with a median scaling procedure. In case multiple samples from different male individuals were available for a given tissue, the median expression value across these samples was used for further analyses. Similarly, frontal cortex and cerebellum expression values were combined into a single median “brain” value.
For the elephant samples we mapped all RNA-seq reads with TopHat 1.4.0 and worked with the unmapped reads only
FPKM values were not calculated for the elphant samples because the reference genome and the annotations have not been published yet
Genome_build: ensembl67 (marmoset), ensembl72 (rat), ensembl73 (wallaby)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
 
Submission date Dec 03, 2013
Last update date May 15, 2019
Contact name Diego Cortez
E-mail(s) diegoclaudio.cortezquezada@unil.ch
Organization name Univerity of Lausanne - CIG
Street address Rue de Lausanne
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL14844
Series (1)
GSE50747 Origins and functional evolution of Y chromosome gene repertoires across the class Mammalia
Relations
BioSample SAMN02429310
SRA SRX386109

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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