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| Status |
Public on Dec 09, 2011 |
| Title |
RV_Wt1 (Wildtype sample 1) |
| Sample type |
SRA |
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| Source name |
wt_heart_right ventricle
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| Organism |
Mus musculus |
| Characteristics |
strain: Mixed background of C57BL/6
genetic variation: Wildtype
development stage: Adult
tissue: Heart, Right ventricle
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 3
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| 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.
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| Submission date |
Dec 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Gladstone Bioinformatics |
| Organization name |
Gladstone Institutes
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| Department |
Data Science and Biotechnology
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| Lab |
Bioinformatics Core
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| Street address |
1650 Owens St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE34274 |
Gene expression profile of right ventricles from adult wild type and Ezh2-deficient hearts |
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| Relations |
| SRA |
SRX110686 |
| BioSample |
SAMN00764127 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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