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Sample GSM846187 Query DataSets for GSM846187
Status Public on Dec 09, 2011
Title RV_Mu3 (Mutant sample 3)
Sample type SRA
Source name Ezh2-deficient_heart_right ventricle
Organism Mus musculus
Characteristics strain: Mixed background of C57BL/6
genetic variation: Ezh2-deficient mutant
development stage: Adult
tissue: Heart, Right ventricle
Extracted molecule total RNA
Extraction protocol Library construction protocol is described in detail in the following paper: Christodoulou, D. C., Gorham, J. M., Herman, D. S. and Seidman, J. 2011. Construction of Normalized RNA-seq Libraries for Next-Generation Sequencing Using the Crab Duplex-Specific Nuclease. Current Protocols in Molecular Biology. 94:4.12.1–4.12.11. Short summary excerpt from the paper: "This unit describes the generation of a normalized RNA-seq library for next-generation sequencing by utilizing the preference of the crab duplex nuclease (DSN) for digesting double-stranded, rather than single-stranded DNA (unit 5.12; also see Zhulidov et al., 2004). In this approach (Basic Protocol), polyadenylated RNA is used to generate a complex RNA-seq library. The library is denatured and incompletely renatured, and then digested with DSN. The kinetics of DNA annealing are such that at any given time abundant DNA molecules are more likely to have re-annealed and become double stranded, while rare molecules are more likely to remain single stranded. Thus, preferentially digesting double-stranded DNA with DSN yields a library markedly enriched for more rare DNA species.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Sample 2
Data processing RNA expression levels: The raw data paired-end FASTQ files were first aligned to mm9 with TopHat 1.2.0 (with the specific command: tophat-1.2.0.Linux_x86_64/tophat --solexa1.3-quals -o <OUTPUT> --segment-mismatches 2 -m 2 --microexon-search -j dcc13/DSAGE/tables/mm9.juncs --butterfly-search -r 185 --mate-std-dev 75 mm9 <FIRST_FASTQ_FILE_IN_PAIR> <SECOND_FASTQ_FILE_IN_PAIR>). Mapped reads were aggregated into gene-level reads using Cufflinks. Differential expression P-values were calculated using the binomial test.
Submission date Dec 08, 2011
Last update date May 15, 2019
Contact name Gladstone Bioinformatics
Organization name Gladstone Institutes
Department Data Science and Biotechnology
Lab Bioinformatics Core
Street address 1650 Owens St
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platform ID GPL13112
Series (1)
GSE34274 Gene expression profile of right ventricles from adult wild type and Ezh2-deficient hearts
SRA SRX110685
BioSample SAMN00764126

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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