|
| Status |
Public on Dec 21, 2020 |
| Title |
Terminal tracheal cells _ Pe2_Dam_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Dam-control processed DNA from adult terminal tracheal cells expressing LT3-Dam in damaged intestine (Pe)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: w-; dSRF-GAL4, UAS-CD8GFP/+; tub-GAL80ts/UAS-LT3-Dam
treatment: treated with bacteria solution (Pe) for 16hrs
tissue: tracheal cells
|
| Treatment protocol |
During the last 16 hrs at 29°C, flies were fed a Sucrose or Sucrose + Pe solution.
|
| Growth protocol |
Animals were crossed at 18°C. F1 progeny were collected every 48 hrs and aged for a further 7 days at 18°C before transferring to 29°C to induce adult restricted Dam protein expression for 24 hrs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
60 midguts with associated TTCs per condition per biological replicate were dissected in cold PBS and stored at -80°C. Genomic DNA was isolated, RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016).
Libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Pe2.gff
|
| Data processing |
Library strategy: DamID-seq
Sequencing data from TaDa experiments were processed using a previously described pipeline (Marshall et al., 2015)
Reads were mapped to release 6.11 of the Drosophila genome.
Transcribed genes were annotated from Pol II binding data using a custom Perl script (available at https://github.com/tonysouthall/Dam-RNA_POLII_analysis).
Ratio files (log2) were then generated from the experimental and Dam-only control data.
Transcribed genes were identified based on meeting a threshold of 1% FDR and > 0.2 log2 ratios.
Genome_build: BDGP6
Supplementary_files_format_and_content: log2 normalised fold changes between the experimental and Dam-only control as a gff file produced by the damidseq_pipeline
|
| |
|
| Submission date |
Dec 20, 2020 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Tony David Southall |
| E-mail(s) |
[email protected]
|
| Organization name |
Imperial College London
|
| Department |
Life Sciences
|
| Lab |
Southall lab
|
| Street address |
South Kensington Campus
|
| City |
London |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE163570 |
Profiling of RNA Pol II occupancy in adult Drosophila terminal tracheal cell using TaDa (Targeted DamID) in context of homeostasis or damaged intestine |
|
| Relations |
| BioSample |
SAMN17124839 |
| SRA |
SRX9708003 |
