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| Status |
Public on Dec 21, 2020 |
| Title |
Profiling of RNA Pol II occupancy in adult Drosophila terminal tracheal cell using TaDa (Targeted DamID) in context of homeostasis or damaged intestine |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Cell-type specific transcriptional profiling is key to understanding cell fate specification, function and adaptation. This is particularly advantageous for studying specific cell types from complex tissues. In this study, we have used ‘TaDa’ (Targeted DamID), a technique that enables profiling of rare cell populations or cells difficult to isolate by conventional methods. Furthermore, TaDa profiling occurs in vivo and isn’t subject to artefacts arising from disruption of the tissues and cell sorting. Here, we profile the genome-wide binding of RNA polymerase II (Pol II) in terminal tracheal cells (TTCs) that are tightly associated with intestinal tissue from adult Drosophila. We compare terminal tracheal transcriptome from control to regenerative intestine in adult fly. Our data reveal new tracheal intrinsic mechanisms that are essential, in this gut-trachea communication, for regulating intestinal stem cell proliferative activity in context of damage. Our study represents the first analysis of terminal tracheal cell transcriptional profiling in context of homeostasis and regenerative adult intestine and provide new insight into the regulatory programs that underlie the complex interactions between gut-neighbourhood.
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| Overall design |
Animals were raised and aged at 18 degrees and shifted to 29 degrees 7 days after eclosion. 24 hours after temperature shift, tissues were collected and frozen. Of to note, during the last 16 hrs at 29°C, flies were fed a Sucrose or Sucrose + Pe solution.Then, Genomic DNA was isolated, RNAseA treated and DpnI digested. Adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of adaptors. Libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. NextSeq™ 500 platform was used. We analysed 8 samples in total. 2 biological replicates were performed for adult terminal tracheal cells in control condition (Suc) and in test condition (Pe).
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| Contributor(s) |
Perochon J, Yu Y, Aughey GN, Southall TD, Cordero JB |
| Citation(s) |
33972729 |
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| Submission date |
Dec 20, 2020 |
| Last update date |
Jun 22, 2021 |
| Contact name |
Tony David Southall |
| E-mail(s) |
[email protected]
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| Organization name |
Imperial College London
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| Department |
Life Sciences
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| Lab |
Southall lab
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| Street address |
South Kensington Campus
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| City |
London |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (8)
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| GSM4981941 |
Terminal tracheal cells _ Pe1_Dam_rep1 |
| GSM4981942 |
Terminal tracheal cells _ Pe1_DamPol_rep1 |
| GSM4981943 |
Terminal tracheal cells _ Pe2_Dam_rep2 |
| GSM4981944 |
Terminal tracheal cells _ Pe2_DamPol_rep2 |
| GSM4981945 |
Terminal tracheal cells _ Suc1_Dam_rep1 |
| GSM4981946 |
Terminal tracheal cells _ Suc1_DamPol_rep1 |
| GSM4981947 |
Terminal tracheal cells _ Suc2_Dam_rep2 |
| GSM4981948 |
Terminal tracheal cells _ Suc2_DamPol_rep2 |
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| Relations |
| BioProject |
PRJNA686784 |
| SRA |
SRP298620 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE163570_Pe1.gff.gff.gz |
4.7 Mb |
(ftp)(http) |
GFF |
| GSE163570_Pe2.gff.gff.gz |
4.5 Mb |
(ftp)(http) |
GFF |
| GSE163570_Suc1.gff.gff.gz |
4.7 Mb |
(ftp)(http) |
GFF |
| GSE163570_Suc2.gff.gff.gz |
4.7 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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