GEO DataSets

(Submitter supplied) During development cells become gradually restricted in their differentiation potential by the repression of alternative cell fates. While we know that the Polycomb complex plays a crucial role in this process, it still remains unclear how alternative fate genes are specifically targeted for silencing in different cell lineages. We address this question by studying Ultrabithorax (Ubx), a multi-lineage transcription factor (TF) of the Hox class, in the mesodermal and neuronal lineages using sorted nuclei of Drosophila embryos and by interfering with Ubx in mesodermal cells that have already initiated differentiation. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

60 Samples

Download data: BED

(Submitter supplied) Transcription Factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

9 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

74 Samples

Download data: BED, TXT

(Submitter supplied) During development cells become gradually restricted in their differentiation potential by the repression of alternative cell fates. While we know that the Polycomb complex plays a crucial role in this process, it still remains unclear how alternative fate genes are specifically targeted for silencing in different cell lineages. We address this question by studying Ultrabithorax (Ubx), a multi-lineage transcription factor (TF) of the Hox class, in the mesodermal and neuronal lineages using sorted nuclei of Drosophila embryos and by interfering with Ubx in mesodermal cells that have already initiated differentiation. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

14 Samples

Download data: TXT

(Submitter supplied) Hox homeodomain transcription factors are key regulators of animal development. They specify the identity of segments along the anterior-posterior body axis in metazoans by controlling the expression of diverse downstream targets, including transcription factors and signaling pathway components. The Drosophila melanogaster Hox factor Ultrabithorax (Ubx) directs the development of thoracic and abdominal segments and appendages, and loss of Ubx function can lead for example to the transformation of third thoracic segment appendages (e.g. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

8 Samples

Download data: TXT

(Submitter supplied) The Hox genes are responsible for generating morphological diversity along the anterior-posterior axis during animal development. The Drosophila Hox gene Ultrabithorax (Ubx), for example, is required for specifying the identity of the third thoracic (T3) segment of the adult, which includes the dorsal haltere, an appendage required for flight, and the ventral T3 leg. Ubx mutants show homeotic transformations of the T3 leg towards the identity of the T2 leg and the haltere towards the wing. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

4 Samples

Download data: BAR, BED, CEL

(Submitter supplied) Hox proteins are transcription factors and key regulators of segmental identity along the anterior posterior axis across all bilateral animals. Despite decades of research, mechanism by which Hox proteins select their targets and specify segmental identity remains elusive. To address this question we carried out whole genome ChIP-chip experiments to identify direct targets of Hox protein Ultrabithorax (Ubx) during haltere development in Drosophila. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4149 GPL4150

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13304 GPL21306

42 Samples

Download data: TXT

(Submitter supplied) We sought to determine the genomic binding profile of the Drosophila Hox protein Ubx in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged Ubx under the control of a metallothionein promoter. Upon Ubx expression, we identified high enrichment of Ubx at a large number transcription start sites that colocalises with the GAGA and M1BP.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

3 Samples

Download data: BED

(Submitter supplied) We sought to determine the genes regulated by the Drosophila Hox protein AbdA in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged AbdA under the control of a metallothionein promoter.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: TXT, XLS

(Submitter supplied) We sought to determine the genomic binding profile of the Drosophila Hox protein AbdA in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged AbdA under the control of a metallothionein promoter. Upon AbdA expression, we identified high enrichment of AbdA at a large number transcription start sites that colocalises with the GAGA and M1BP. Genes targeted by GAGA and M1BP contain paused RNA polymerase II and show enrichment of PcG proteins. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13304 GPL21306

33 Samples

Download data: BED, BIGWIG

(Submitter supplied) We have developed SpyChIP, a method that depends on covalent isopeptide bond formation, to identify sites of cell type-specific transcription factor (TF) occupancy in native physiological contexts without tissue dissociation or nuclei sorting. Using SpyChIP, we characterized the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two non-overlapping domains of the Drosophila haltere imaginal disc, revealing extensive region-specific Ubx-DNA binding events. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

16 Samples

Download data: BIGWIG

(Submitter supplied) Hox genes regionalize the animal body axis by modifying complex morphogenetic and differentiation processes during development. The transformation of wings into halteres by the Hox gene Ultrabithorax (Ubx) in Drosophila melanogaster presents an excellent model system to study the transcriptional networks that control such complex developmental programmes. We have employed an inducible misexpression system to switch on Ubx in the wing epithelium at successive larval, prepupal and pupal stages, and have used microarray expression profiling to identify the primary transcriptional responses to Ubx. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

48 Samples

Download data: CEL

(Submitter supplied) We profiled the chromatin accessibility, transcription factor binding, and gene expression in the homologous wing and haltere imaginal disc of Drosophila melanogaster, which are distinguished by the expression of the Hox protein Ultrabithorax (Ubx). Through the analysis of chromatin changes, we show Ubx has widespread effects on the chromatin landscape to specify cell identity.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

36 Samples

Download data: BIGWIG, CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9151

14 Samples

Download data: GTF, XLS

(Submitter supplied) Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. more...

Organism:

Bombyx mori

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9151

12 Samples

Download data: BED, XLS

(Submitter supplied) Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. more...

Organism:

Bombyx mori

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9151

2 Samples

Download data: DIFF, GTF

(Submitter supplied) To gain insights into the species-specific events downstream of Ubx, we identified direct targets of Ubx from Apis by ChIP-seq and compared them with those of Drosophila at the level of both their function and regulation. While the majority of the targets are species-specific, the ontological distribution of all targets was similar amongst the two species. Interestingly, although considerable number of wing-patterning genes are retained as targets of Ubx over the past 300 millions years, many of them are differentially expressed only between wing and haltere in Drosophila and not between forewing and hindwing in Apis . more...

Organism:

Apis mellifera

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13725

12 Samples

Download data: TXT

(Submitter supplied) Although the majority of genomic binding sites for the insulator protein CTCF are constitutively occupied, a subset show variable occupancy. Such variable sites provide an opportunity to assess context-specific CTCF functions in gene regulation. Here we have identified a variably occupied CTCF site in the Ultrabithorax (Ubx) gene in Drosophila. This site is occupied in tissues where Ubx is active (third thoracic imaginal leg disc) but is not bound in tissues where the Ubx gene is repressed (first thoracic imaginal leg disc).

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15641

4 Samples

Download data: PAIR, SGR, TXT

(Submitter supplied) Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here, we demonstrate that high-throughput in vitro DNA binding assays coupled with unbiased computational analysis provide unprecedented insight into how different DNA sequences select distinct compositions and configurations of homeodomain TF complexes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL19132 GPL13304

33 Samples

Download data: BED, BW, HIC