|
| Status |
Public on Jul 01, 2016 |
| Title |
Input-ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
eye-antennal discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Bloomington 42269
genotype/variation: Grh-GFP
age: 3rd instar
tissue: eye-antennal discs
|
| Treatment protocol |
Wandering 3rd instar larvae were dissected in PBS to extract the eye-antennal discs
|
| Growth protocol |
All flies were raised at 25˚C on standards fly food
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated chromatin was extracted using an anti-GFP ab and immunocomplexes were recovered on A/G megnetic beads
ChIP libraries were prepared using the Truseq DNA library prep kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Cleaning (fastq-mcf)
Mapping to dm3 genome using bowtie2
Calling peaks using macs2
Calling differential peaks between Dac-ChIP and input (macs2)
Filtering out all promoter regions using Bedtools
Genome_build: Drosophila melanogaster FlyBase version 5
Supplementary_files_format_and_content: Bed file with Narrow peaks called by macs2; Bed file of filtered peaks ( no 5'UTR or 1kb upstream of TSS)
|
| |
|
| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jelle Jacobs |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of molecular Pathology
|
| Department |
VBC
|
| Lab |
Stark lab
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE82151 |
Dachshund ChIP-seq in Drosophila Melanogaster 3rd instar imaginal eye discs |
|
| Relations |
| BioSample |
SAMN05197883 |
| SRA |
SRX1816637 |
