Genomics,Multiomics

Dataset Information

2

Profiling of RNA Pol II occupancy in Drosophila neural stem cell populations using TaDa (Targeted DamID)


ABSTRACT: Cell-type specific transcriptional profiling is key to understanding cell fate specification and function. In order to achieve this it has been necessary, to date, to isolate specific cell types from complex tissues. We have developed 'TaDa', a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation or affinity purification. The method is simple, sensitive, highly reproducible and is in principle transferable to any model system. Here we show that TaDa can be used to identify transcribed genes in a cell-type specific manner. We profile the genome-wide binding of RNA polymerase II (Pol II) in adjacent, clonally related neural stem cells in intact Drosophila brains. Our data reveal the activity of non-canonical metabolic pathways in proliferating neuroepithelial cells, and highlight a possible role for the retinal determination gene regulatory network in patterning neural stem cell fates. We also identify temporal differences in the activity of signalling pathways that control neuroepithelial cell fate by profiling Pol II occupancy at two different stages of brain development. Using RNA Pol II TaDa to profile, in a cell-type specific manner, the transcriptional state of neuroepithelial cells at two stages of larval brain development. Closely related asymmetrically dividing neural stem cells (neuroblasts) were also profiled, in order to compare the transcriptomes of two different types of neural stem cells. 3 biological relicates were performed for 3rd instar neuroepithelial cells (with one dye-swap). 2 biological relicates were performed for 3rd instar neuroblasts (with dye-swap). 2 biological relicates were performed for 1st instar neuroepithelial cells (with dye-swap). As additional supporting evidence for the Pol II TaDa technique, 2 biological relicates were performed for 3rd instar salivary glands (with dye-swap) in order to compare with previous Pol II-ChIP data for this tissue [PMID 22821985].

OTHER RELATED OMICS DATASETS IN: PRJNA202424

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Tony D Southall   Tony David Southall  Andrea H Brand 

PROVIDER: E-GEOD-46803 | ArrayExpress | 2013-06-21

SECONDARY ACCESSION(S): GSE46803PRJNA202424

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-46803.idf.txt Idf
E-GEOD-46803.processed.1.zip Processed
E-GEOD-46803.raw.1.zip Raw
E-GEOD-46803.raw.2.zip Raw
E-GEOD-46803.raw.3.zip Raw
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Publications

Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells.

Southall Tony D TD   Gold Katrina S KS   Egger Boris B   Davidson Catherine M CM   Caygill Elizabeth E EE   Marshall Owen J OJ   Brand Andrea H AH  

Developmental cell 20130620 1


Cell-type-specific transcriptional profiling often requires the isolation of specific cell types from complex tissues. We have developed "TaDa," a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation, or affinity purification. The method is simple, sensitive, highly reproducible, and transferable to any model system. We show that TaDa can be used to identify transcribed genes  ...[more]

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