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Sample GSM1054988 Query DataSets for GSM1054988
Status Public on Feb 17, 2015
Title aca.lv.3
Sample type SRA
 
Source name Acomys cahirinus_liver
Organism Acomys cahirinus
Characteristics strain (source): in-house colony
genotype/variation: wild type
age: adult
tissue: normal liver
organ part: whole liver
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNAeasy (Qiagen) purification kit according to the manufacturer’s instructions. RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina, Inc.) in accordance with the manufacturer' instructions. Polyadenylated RNA was isolated using a poly-dT bead procedure, chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 300-bp fragments were excised and then PCR-amplified (20 cycles). After column purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalysers.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description biological replicate 3
Data processing The RNA-seq libraries were each sequenced (76 cycles) in at least one lane of the Illumina Genome Analyser IIx platform.
Samples were demultiplexed and the indexed adapter sequences were trimmed using the CASAVA v1.8.2 software (Illumina, Inc.).
The fluorophore intensity files were analyzed with the standard Illumina base-calling algorithms.
51-bp paired-end reads that passed the chastity filter threshold were mapped using TopHat4 2.0 with default parameter values, except for distance between mature pairs (r=200) and the number of allowable mismatches between read and genomic sequences (n=3) to ensure possible genetic heterogeneity between populations. The anchor size (i.e. the minimum aligned length spanning each of the two exons that define a splice junction) was set at 8 bp, and we allowed 1 mismatch on the anchor region. The transcript isoform abundance and averaged gene expression levels were calculated and FPKM normalized using Cufflinks.
Genome_build: Bos taurus Ensembl genome build 62,
Capra hircus de novo transcriptome assembly (PRJNA182763); see GSE43013_chi.rna.gtf.
Sus scrofa Ensembl genome build 62
Canis familiaris Ensembl genome build 62
Felis catus Ensembl genome build 62
Meles meles de novo transcriptome assembly (PRJNA182767)
Ursus americanus de novo transcriptome assembly (PRJNA182773)
Murina leucogaster de novo transcriptome assembly (PRJNA182766)
Tadarida brasiliensis de novo transcriptome assembly (PRJNA182772)
Petaurus breviceps de novo transcriptome assembly (PRJNA182769)
Erinaceus europaeus Ensembl genome build 62
Oryctolagus cuniculus Ensembl genome build 62
Equus caballus Ensembl genome build 62
Chlorocebus aethiops de novo transcriptome assembly (PRJNA182762)
Acomys cahirinus de novo transcriptome assembly (PRJNA182705)
Cavia porcellus Ensembl genome build 62
Mesocricetus auratus de novo transcriptome assembly (PRJNA182765)
Meriones unguiculatus de novo transcriptome assembly (PRJNA182768)
Mus musculus Ensembl genome build 62
Peromyscus leucopus de novo transcriptome assembly (PRJNA182770)
Rattus norvegicus Ensembl genome build 62
Tamias sibiricus de novo transcriptome assembly (PRJNA183188)
Suncus murinus de novo transcriptome assembly (PRJNA182771).
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
 
Submission date Dec 19, 2012
Last update date May 15, 2019
Contact name Alexey Fushan
E-mail(s) alexfushan@gmail.com
Organization name EWHA
Street address 52, Ewhayeodae-gil
City Seoul
State/province Seodaemun-gu
ZIP/Postal code 120-750
Country South Korea
 
Platform ID GPL16396
Series (1)
GSE43013 Gene Expression Defines Natural Changes in Mammalian Lifespan
Relations
SRA SRX211578
BioSample SAMN01831855

Supplementary file Size Download File type/resource
GSM1054988_aca.lv.3.txt.gz 54.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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