|
| Status |
Public on Jun 30, 2020 |
| Title |
Psi DamID 3 |
| Sample type |
SRA |
| |
|
| Source name |
imaginal wing disc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
gal4 driver: sdGAL4 ; tsGAL80
stock number: BL8609; BL7019
developmental stage: mid-third instar larvae
tissue: wing imaginal disc
Sex: female
dam only sample used as control: sdGAL4_Dam1
|
| Treatment protocol |
Dam-fusion contructs expressed using scalloped-GAL4 driver in the background of temperature-sensitive GAL80
|
| Growth protocol |
Drosophila melanogaster embryos from parental crosses were collected over the course of <4-hour lays at 25ºC, after which the embryos were placed at the repressive temperature of 18ºC for 7 days until the second larval instar stage. The larvae were then shifted to the permissive temperature of 29ºC for 24h
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Wing discs from female larvae were collected into cold PBS, genomic DNA was extracted using a Zymo Quick-DNA kit (#D4069). DNA was digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 300bp using Covaris ME200 sonicator and DamID adaptors removed via AlwI digestion. Sonicated material was end-repaired, adenylated, sequencing adaptors were ligated and samples were PCR amplified.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
control
|
| Data processing |
Library strategy: DamID
FASTQ files were processed with damidseq_pipeline v1.4.5, including aligning the reads to the Drosophila BDGP6 genome with Bowtie2, converting to GATC resolution and calculating the log2 ratio between Dam-fusion protein profile and Dam alone
Average enrichment across biological replicates was determined by calculating average coverage at each region flanked by GATC sites, and the average profile was used for further analysis.
Significant peaks were detected at 1% FDR using the find_peaks script
Genome_build: BDGP6
Supplementary_files_format_and_content: Bedgraph file indicating average enrichment at each GATC-flanked genomic fragment. Score represents the normalised log2(Dam-fusion/Dam) enrichment.
Supplementary_files_format_and_content: GFF file containing peak coordinates identified the corresponding bedgraph profile at FDR0.01, the average enrichment across the peak region and the FDR value
|
| |
|
| Submission date |
May 01, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Olga Zaytseva |
| E-mail(s) |
olga.zaytseva@anu.edu.au
|
| Organization name |
John Curtin School of Medical Research
|
| Street address |
131 Garran Road
|
| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE149718 |
Identification of genome-wide binding sites of Psi, Myc and Pol in Drosophila imaginal wing discs using Targeted DamID |
| GSE149721 |
Identification of genome-wide binding sites of Psi, Myc and Pol and gene expression following Psi or Myc knockdown in Drosophila larval wing tissue |
|
| Relations |
| BioSample |
SAMN14791456 |
| SRA |
SRX8241413 |
