|
| Status |
Public on Jul 01, 2017 |
| Title |
Dsim-ref-2 |
| Sample type |
SRA |
| |
|
| Source name |
embryos
|
| Organism |
Drosophila simulans |
| Characteristics |
Stage: 4-8hr embryo
|
| Growth protocol |
Flies were reared on standard medium at 25C, 12hr/12hr light and dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were collected on standard apple juice plate. Before collection, pre-collection for 1hr was performed. Embryos were then collected for 4 hours and aged for 4 hours in 25C. ChIP was performed following standrad modEncode protocol.
Illumina TreSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
raw reads were pre-processed with trim-galore to remove adatoprs and low quality bases
processed reads were mapped to reference genomes with TopHat
read counts for each gene were generated by htseq-count
Genome_build: D. melanogaster release 6 (fly base), D.simulans release 2 (fly base)
Supplementary_files_format_and_content: read counts for the exons of each gene
|
| |
|
| Submission date |
Feb 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Grace Yuh Chwen Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Irvine
|
| Street address |
UCI
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92617 |
| Country |
USA |
| |
|
| Platform ID |
GPL13306 |
| Series (2) |
| GSE94741 |
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution [RNA-seq] |
| GSE94742 |
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution |
|
| Relations |
| BioSample |
SAMN06318509 |
| SRA |
SRX2548615 |
