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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 19, 2014 |
| Title |
DEN treated WT replicate 1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/CBA
age: 8 months
genotype: WT
tissue: liver
agent: 25ml per kg DEN (diethyl nitrosamine)
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| 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 files containing normalized read counts for each gene.
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| Submission date |
Sep 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Iannis Talianidis |
| E-mail(s) |
talianid@imbb.forth.gr
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| Organization name |
Foundation for Research and Technology - Hellas
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| Department |
Institute of Molecular Biology and Biotechnology
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| Street address |
100 N. Plastira Str
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| City |
Vassilika Vouton, Herakleion |
| State/province |
Crete |
| ZIP/Postal code |
70013 |
| Country |
Greece |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE49555 |
PR-SET7 inactivation causes hepatocyte necrosis and spontaneous development of hepatocellular carcinoma derived from ductal progenitor cells |
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| Relations |
| BioSample |
SAMN03074548 |
| SRA |
SRX706569 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1508277_DEN_WT_BR1.txt.gz |
138.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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