|
| Status |
Public on Jul 01, 2017 |
| Title |
Dsim-Ref-INPUT1 |
| Sample type |
SRA |
| |
|
| Source name |
embryos
|
| Organism |
Drosophila simulans |
| Characteristics |
Stage: 4-8hr embryo
chip antibody: none
|
| Treatment protocol |
N/A
|
| Growth protocol |
Flies were reared on standard medium at 25C, 12hr/12hr light and dark cycle
|
| Extracted molecule |
genomic DNA |
| 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.
Library was prepared using NuGen Ovation Ultralow Library Systems V2
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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 bwa
reads with mapping quality score smaller than 30 were filtered using samtools
fold enrichment (IP with respect to matching INPUT) tracks were generated using MAC2
Genome_build: D. melanogaster release 6 (fly base), D.simulans release 2 (fly base)
Supplementary_files_format_and_content: bigWig
|
| |
|
| 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) |
| GSE94735 |
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution [ChIP-seq] |
| GSE94742 |
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution |
|
| Relations |
| BioSample |
SAMN06318446 |
| SRA |
SRX2548352 |
