NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1201705 Query DataSets for GSM1201705
Status Public on Aug 01, 2014
Title PR-SET7_LOBE replicate 3
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics strain: C57BL6/CBA
age: 8 months
genotype: PR-SET7_LX_ALB_CRE
tissue: liver
Growth protocol Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) and water ad libitum
Extracted molecule total RNA
Extraction protocol Approximately 20 µg of total RNAs were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (Life Technologies, Carlsbad, CA, USA)
The isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Data processing Base calling was performed using software provided with the Ion Proton sequencer.
Sequenced reads were trimmed for adaptor sequence and mapped to mm9 whole genome using tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html)
Tags overlapping the Ensembl build 67 mouse exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized using EDASeq and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file containing normalized counts for each gene with length greater than 500bp and at least 1 read in at least 1 sample.
 
Submission date Aug 05, 2013
Last update date May 15, 2019
Contact name Iannis Talianidis
E-mail(s) talianid@imbb.forth.gr
Organization name Foundation for Research and Technology - Hellas
Department Institute of Molecular Biology and Biotechnology
Street address 100 N. Plastira Str
City Vassilika Vouton, Herakleion
State/province Crete
ZIP/Postal code 70013
Country Greece
 
Platform ID GPL18635
Series (1)
GSE49555 PR-SET7 inactivation causes hepatocyte necrosis and spontaneous development of hepatocellular carcinoma derived from ductal progenitor cells
Relations
BioSample SAMN02302963
SRA SRX331687

Supplementary file Size Download File type/resource
GSM1201705.txt.gz 139.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap