Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression profiling of isolated dendritic arborization (da) neurons of Drosophila

ABSTRACT: Paper abstract: The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of isolated these neurons. Their profiles were similarly enriched in cell-type-specific enhancers of genes implicated in neural development. We identified a total of 429 target genes, of which 56 were common to Ab and Kn; these targets included genes necessary to shape dendritic arbors in either or both of the two sensory subtypes. Furthermore, a common target gene, encoding the cell adhesion molecule Ten-m, was expressed more strongly in class I than IV, and this differential was critical to the class-selective directional control of dendritic branch sprouting or extension. Our analyses illustrate how differentiating neurons employ distinct and shared repertoires of gene expression to produce class-selective morphological traits. da neurons were isolated by magnetic bead sorting from larvae of the following three genotypes and obtained genome-wide expression profiles: larvae expressing a cell-surface marker mCD8:GFP alone (Control), and larvae ectopically expressing Abrupt (Ab ME) or Knot (Kn ME) together with mCD8:GFP in all classes of da neurons. 3 biological replicates were collected.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Yukako Hattori

PROVIDER: E-GEOD-38660 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

DamID profiling of neural transcription factor (Abrupt and Knot) binding in Drosophila melanogaster embryos

Project description:Paper abstract: The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of isolated these neurons. Their profiles were similarly enriched in cell-type-specific enhancers of genes implicated in neural development. We identified a total of 429 target genes, of which 56 were common to Ab and Kn; these targets included genes necessary to shape dendritic arbors in either or both of the two sensory subtypes. Furthermore, a common target gene, encoding the cell adhesion molecule Ten-m, was expressed more strongly in class I than IV, and this differential was critical to the class-selective directional control of dendritic branch sprouting or extension. Our analyses illustrate how differentiating neurons employ distinct and shared repertoires of gene expression to produce class-selective morphological traits. Each Dam-fusion-derived sample is compared to a control Dam-only sample. Four biological replicates were performed.

2013-11-27 | E-GEOD-38659 | biostudies-arrayexpress

Expression profiling of isolated dendritic arborization (da) neurons of Drosophila

2013-11-27 | GSE38660 | GEO

DamID profiling of neural transcription factor (Abrupt and Knot) binding in Drosophila melanogaster embryos

2013-11-27 | GSE38659 | GEO

Microarray gene expression profiling of isolated class I and class IV Drosophila dendritic arborization sensory neurons

Project description:Class I and IV Drosophila dendritic arborization sensory neurons were isolated via magnetic bead sorting and total RNA isolated from the samples was used for gene expression profiling. Elucidating the molecular mechanisms controlling dendrite development is key to understanding the pivotal role these structures play in influencing synaptic integration and neural function. Despite significant advances in this field, genetic pleiotropy remains a significant impediment to investigating such complex developmental processes. To circumvent this problem, we have applied class specific neuron transcriptional expression profiling coupled to an in vivo RNAi functional validation screen in order to dissect the molecular bases of Drosophila class I and class IV dendritic arborization (da) neuron dendritogenesis. Gene expression profiling of class I and IV da neurons, isolated via magnetic bead sorting (using protocols as described in Iyer et al., 2009), was performed at the third instar larval stage of development from independent cell isolations from 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of either GAL4ppk.1.9 driver or Gal80ppk; GAL4221. For controls, age matched whole larval homogenate RNA was used.

2013-07-21 | E-GEOD-46154 | biostudies-arrayexpress

Transcriptional Profiling of Class IV da Neurons

Project description:Elucidating the molecular mechanisms controlling dendrite development is key to understanding the pivotal role these structures play in influencing synaptic integration and neural function. Despite significant advances in this field, genetic pleiotropy remains a significant impediment to investigating such complex developmental processes. To circumvent this problem, we have applied class specific neuron transcriptional expression profiling coupled to an in vivo RNAi functional validation screen in order to dissect the molecular bases of Drosophila class IV dendritic arborization (da) neuron dendritogenesis. Microarray analyses reveal transcriptional regulation as one highly enriched biological and functional category with 420 transcription factors significantly expressed in class IV neurons. Among these, we identify roles for 268 genes in mediating a broad spectrum of functions including dendritic field coverage, branching, routing, and tiling. Collectively, our analyses provide a more comprehensive framework of the role complex transcriptional networks play in directing distinct aspects of class specific dendrite morphogenesis. Gene expression profiling of class IV da neurons performed at the third instar larval stage of development from two independent cell isolations from 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL4ppk.1.9 driver

2014-04-01 | E-GEOD-28675 | biostudies-arrayexpress

Branching Gene Regulatory Network for Neurotransmitter versus Axonal Pathfinding

Project description:In previous studies we found that the two transcription factors collier (FB:knot, kn) [vertebrate Ebf1] and ladybird early (lbe) [vertebrate Lbx1/2], when co-misexpressed from elav-Gal4, generate ectopic Nplp1 neuropeptidergic cells in the entire ventral nerve cord during Dmel. embryonic development. We also found that the axon generated by the ectopic Nplp1 cells, seem to follow the same fascicle as the wild type Nplp1 neurons. Therefore we used RNA-seq on control and UAS‑col,lbe co-misexpression to find candidate factors important in axon pathfinding of the Nplp1 neurons. We also included single misexpression of UAS-col and UAS-lbe, together with co-misexpression of UAS-ap, eya, since we know that col and lbe activate those two factors during the cell fate specification of Nplp1 neurons.

2019-03-11 | GSE113260 | GEO

Identification of genes enriched in nociceptive neurons of Drosophila larvae

Project description:This study aims to identify genes whose expression is enriched in the nociceptive neurons of Drosophila larvae. These neurons are involved in detecting noxious mechanical and noxious thermal stimuli. Four replicates each for Class I md-da neurons (2-21Gal4>>UAS-mCD8GFP) and Class IV md-da (ppk-GAL4>>UAS-mCD8GFP) neurons were analyzed. RNA from 50-60 neurons for each replicate was isolated by laser capture microdissection. RNA was amplified using the WT-Ovation Pico Kit from NuGen technologies. RNA was fragmented and labeled using the FL-Ovation cDNA Biotin Module V2 (NuGen Technologies). RNA was hybridized to arrays and data scanned at the Translational Genomics Research Institute.

2016-03-06 | E-MTAB-3863 | biostudies-arrayexpress

Abrupt scrib- vs. Abrupt and RasV12 (RasACT) scrib-, NotchICD (NACT) scrib- +/- JNK (Bsk) expression profiles

Project description:Drosophila mosaic eye-antennal discs from the listed genotypes generated using the MARCM system were dissected from 3rd instar larvae at day 5 after egg deposition. 20 pairs of discs for the Abrupt and scrib- + Abrupt samples and 50 pairs from FRT control, NACT scrib- +/- BskDN and RasACT scrib- +/- BskDN were used to prepare RNA. Samples were prepared in triplicate, and the RNA isolated using TRIZOL, before being column purified (Qiagen). Probes were hybridized to GeneChip Drosophila 2.0 Genome Arrays (Affymetrix). To compare the expression profile of Abrupt when overexpressed in the eye-antennal discs with tumours formed by Abrupt overexpression in scrib- clones, and to reveal JNK responsive genes in RasV12 (RasACT) scrib- versus NotchICD (NACT) scrib- eye-antennal mosaic discs

2013-08-15 | E-GEOD-42938 | biostudies-arrayexpress

Abrupt scrib- vs. Abrupt and RasV12 (RasACT) scrib-, NotchICD (NACT) scrib- +/- JNK (Bsk) expression profiles

2013-08-15 | GSE42938 | GEO

Combinatorial transcriptional regulation modulates cytoskeletal-mediated dendritic arbor development

Project description:Transcription factors (TFs) have emerged as essential cell autonomous mediators of subtype specific dendritogenesis, however, the downstream effectors of these TFs remain largely unknown, as are the cellular events that TFs control to direct morphological change. As dendritic morphology is largely dictated by the organization of the actin and microtubule (MT) cytoskeletons, elucidating TFmediated cytoskeletal regulatory programs is key to understanding molecular control of diverse dendritic morphologies. Previous studies in Drosophila melanogaster have demonstrated that the conserved TFs Cut and Knot exert combinatorial control over aspects of dendritic cytoskeleton development, promoting actin and MTbased arbor morphology, respectively. To investigate transcriptional targets of Cut and/or Knot regulation, we conducted systematic neurogenomic studies, coupled with in vivo genetic screens utilizing multi-fluor cytoskeletal and membrane marker reporters. These analyses identified a host of putative Cut and/or Knot effector molecules and a subset of these putative TF targets converge on modulating dendritic cytoskeletal architecture and are grouped into three major phenotypic categories, based upon neuromorphometric analyses:¬¬ complexity enhancer, complexity shifter, and complexity suppressor. Complexity enhancer genes normally function to promote higher order dendritic growth and branching with variable effects on MT stabilization and F-actin organization, whereas complexity shifter and complexity suppressor genes normally function in regulating proximal-distal branching distribution or in restricting higher order branching complexity, respectively, with spatially restricted impacts on the dendritic cytoskeleton. Collectively, we implicate novel genes and cellular programs by which TFs distinctly and combinatorially govern dendritogenesis via cytoskeletal modulation.

2017-10-10 | GSE83938 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data