|
| Status |
Public on Sep 10, 2011 |
| Title |
Simulated Condition 1, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
C1 (simulated S2)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Simulated unstranded Paired-end RNA-Seq . Mean fragment length = 180bp, std. dev. = 20bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
C1_R3
|
| Data processing |
TopHat and Cufflinks. Total sequencing yield for each replicate was chosen to match that of the real S2 data. Each replicate was mapped to the fly genome with TopHat v 1.3.1 seperately. The replicates were assembled seperately with Cufflinks v 1.1.0. The replicate assemblies were merged with Cuffmerge. This merged assembly was then analysed for differentially expressed and regulated genes with Cuffdiff.
|
| |
|
| Submission date |
Sep 09, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Cole Trapnell |
| E-mail(s) |
cole@broadinstitute.org
|
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology
|
| Lab |
John Rinn
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE32038 |
Differential Gene and Transcript Expression Analysis with TopHat and Cufflinks |
|
| Relations |
| BioSample |
SAMN02198127 |
