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Sample GSM1278046

Query DataSets for GSM1278046

Status

Public on Apr 15, 2014

Title

elephant RNAseq data 3

Sample type

SRA

Source name

fibroblast

Organism

Loxodonta africana

Characteristics

tissue: fibroblast
Sex: male
individuals: individual 2

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

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