|
| Status |
Public on Nov 08, 2012 |
| Title |
Dyak_WPP_RNAseq_3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal white prepupa
|
| Organism |
Drosophila yakuba |
| Characteristics |
developmental stage: white prepupa
|
| Growth protocol |
The three sequenced inbred fly lines for the different Drosophila species are grown in room temperature on standard fly food. The white prepupa whole animals are collected within 15 min time interval.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples are isolated using Trizol Chroloform, followed by QIAGEN column purification.
RNA seq libraries are prepared using standard Illumina single end RNA seq library protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Sample 9
|
| Data processing |
Sequencing data are mapped to the genome as well as the annotated exon-exon conjunctions using Bowtie, allowing 2 mismatches.
Only uniquely mapped reads were used to generate the read counts and RPKM values for each gene following the methods described in Mortazavi et al 2008 Nature Methods paper.
Genome_build: dm3, droSim1, droYak2
Supplementary_files_format_and_content: tab delimited file including read counts and RPKM values for each gene (abundance measurements)
|
| |
|
| Submission date |
Nov 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Institute for Genomics and Systems Biology
|
| Street address |
900 E. 57th STR. 10th FL.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platform ID |
GPL11000 |
| Series (1) |
| GSE24449 |
Genome-wide comparative ChIP-seq data of CTCF and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer |
|
| Relations |
| SRA |
SRX203265 |
| BioSample |
SAMN01803800 |
