|
| Status |
Public on Mar 20, 2023 |
| Title |
Gr5a_DamPcl_CD+OSMI-1 |
| Sample type |
SRA |
| |
|
| Source name |
Gr5a sensory neurons
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Gr5a sensory neurons
dietary condition: Control diet + 10uM OSMI-1
genotype: Gr5a;tubulinGAL80ts>UAS-LT3-Dam::Pcl
|
| Treatment protocol |
Flies were placed either on a control diet (5% sucrose) or sugar diet (30% sucrose). Both diets were supplemented with 10 uM OSMI-1 dissolved in 10 % DMSO
|
| Growth protocol |
Flies were grown at 19-20C. Male and feamle age-matched flies were collected 2 days after eclosure and housed in vials of 35. Flies were placed on their specific dietary condition in 20C. At day 5 flies were mover to 28C until day 6 afor an additional day to induce Dam. Samples were collected and DNA isolated.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Three biological replicates were used for each condition, and each replicate consisted of 300 heads. For tissue collections, briefly heads were collected using pre-chilled sieves in liquid nitrogen on dry ice. Frozen heads were then lysed. DNA was extracted from frozen heads following kit instructions. For identification of methylated regions briefly, purified DNA was digested by DpnI followed by PCR purification of digested sequences. TaDa adaptors were ligated by T4 DNA ligase . Adapter ligated DNA was PCR amplified according to protocol, and subsequently purified. Purified DNA was digested with DpnII followed by sonication to yield fragments averaging 200-300bp. TaDa adaptors were removed from sonicated DNA by digestion.
Libraries were generated using the Takara ThruPlex kit (cat #022818) using 3ng input and 10 cycles of PCR. All libraries were sequenced on the Illumina NextSeq platform (High-output kit v2 75 cycles).
DNA-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sonicated DNA
processed by converting normalized log2(Dam-Pcl/Dam) ratio files to bigwig
|
| Data processing |
Reads were aligned using Bowtie2
Reads are extended to 300bp or closest GATC
Bam output is used to generate the ratio file between Dam::Pcl and Dam in bedgraph format
Ratio files were converted to bigwig normalized to 1X genome
Peaks were identified from log2(Dam::Pcl/Dam) ratio files using find_peaks (FDR<0.01)
Genome_build: BDGP6
|
| |
|
| Submission date |
Nov 13, 2021 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Monica Dus |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Street address |
1105 N University, 4224
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE188755 |
A nutrient information pathway links diet to taste (DNA-Seq II) |
| GSE188757 |
Nutrigenomic regulation of sensory plasticity |
|
| Relations |
| BioSample |
SAMN23131971 |
| SRA |
SRX13130728 |
