|
Status |
Public on Aug 17, 2013 |
Title |
D. melanogaster RNA-seq |
Sample type |
SRA |
|
|
Source name |
Whole animal
|
Organism |
Drosophila yakuba |
Characteristics |
developmental stage: White prepupa organism: Drosophila yakuba
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated with Trizol. RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer |
|
|
Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence (using fastx_clipper -a GATCGGAAGAGC -M 12 -Q 33), then mapped to the appropriate whole genome using tophat (tophat -o dmel_WPP --solexa1.3-quals -p 8 --bowtie1 -n 2 -g 1 -M -G dmel.gtf). Duplicated reads were removed with SAMtools rmdup command (with -s flag for single-end data). FPKMs for each gene were calculated using the cufflinks software (cufflinks -b -u). Genome_build: dm3 (D. melanogaster), droSim1 (D. simulans), droYak2 (D. yakuba), dp4 (D. pseudoobscura) Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample. Format is cufflinks standard.
|
|
|
Submission date |
Aug 16, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Kevin White |
Organization name |
University of Chicago
|
Department |
Institute for Genomics and Systems Biology
|
Lab |
Kevin White lab
|
Street address |
900 E. 57th St. Room 10100
|
City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60637 |
Country |
USA |
|
|
Platform ID |
GPL11000 |
Series (1) |
GSE49945 |
Genome-wide comparative ChIP-seq data of H3K27me3 and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer |
|
Relations |
BioSample |
SAMN02318562 |
SRA |
SRX336060 |