Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell type-specific gene expression profiling of Drosophila neurons [RNA-Seq]

ABSTRACT: Gene expression profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Gene expression profiles were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons in the adult Drosophila head using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Sequencing was performed with an Illumina HiSeq 2000.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Fred Davis

PROVIDER: E-GEOD-37027 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Cell type-specific genomics of Drosophila neurons.

Henry Gilbert L GL Davis Fred P FP Picard Serge S Eddy Sean R SR

Nucleic acids research 20120801 19

Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell, 18, 1030-1040; Steiner,F.A., Talbert,P.B., Kasinathan,S., Deal,R.B. and Henikoff,S. (2012) Cell-type-specific nuclei purification f ...[more]

PMID: 22855560

Similar Datasets

Cell type-specific gene expression and chromatin profiling of Drosophila neurons

Project description:This SuperSeries is composed of the following subset Series: GSE37027: Cell type-specific gene expression profiling of Drosophila neurons [RNA-Seq] GSE37032: Cell type-specific chromatin profiling of Drosophila neurons [ChIP-Seq] Refer to individual Series

2012-08-01 | E-GEOD-37033 | biostudies-arrayexpress

Cell type-specific chromatin profiling of Drosophila neurons [ChIP-Seq]

Project description:Chromatin profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Cell type-specific histone modification maps were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Three histone modifications were profiled: H3K4me3, H3K27ac, and H3K27me3. Sequencing was performed with an Illumina HiSeq 2000.

2012-08-02 | E-GEOD-37032 | biostudies-arrayexpress

Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons

Project description:Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability. Here, we considered a well-defined, canonical neuronal population â hippocampal CA1 pyramidal cells â and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population

2016-01-05 | E-GEOD-67403 | biostudies-arrayexpress

IL-33 markedly induces murine eosinophil gene transcription via autocrine IL-4-dependent and -independent mechanisms

Project description:Eosinophils are major effector cells in type 2 inflammatory responses and become activated in response to IL-4 and IL-33, yet the molecular mechanism remains unclear. We examined the direct effect of these cytokines on eosinophils and demonstrated that murine eosinophils respond to IL-4 and IL-33 by phosphorylation of STAT-6 and NFkB, respectively. RNA sequencing analysis of murine eosinophils indicated that IL-33 regulates 519 genes, whereas IL-4 regulates only 28 genes, including 19 IL-33-regulated genes. Interestingly, IL-33 induced eosinophil activation via two distinct mechanisms, IL-4 independent and IL-4 secretion/auto-stimulation dependent. Anti-IL-4 or anti-IL-4Ra antibody-treated eosinophils, as well as Il4- or Stat6-deficient eosinophils, had attenuated protein secretion of a subset of IL-33-induced genes, including Retnla and Ccl17. However, the induction of most IL-33-regulated transcripts (e.g. Il6 and Il13) was IL-4 independent and blocked by NFkB inhibition. Indeed, IL-33 induced the rapid release of pre-formed IL-4 protein from eosinophils by an NFkB-dependent mechanism. Thus, we have identified a novel activation pathway in murine eosinophils that is induced by IL-33 and differentially dependent upon IL-4. These data suggest that IL-4 plays a critical role in auto-amplification of IL-33-induced eosinophil activation and could be a potential target for therapeutic approaches in IL-33-related eosinophil-associated diseases. Low density bone marrow derived murine eosinophils were generated in culture over the period of 14 days. Eosinophils were activated by either IL-33 or IL-4 at 10 ng/ml for 1hr and 4hr. RNA was collected and subjected to next generation sequencing.

2013-08-01 | E-GEOD-43660 | biostudies-arrayexpress

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Project description:We developed an affinity purification approach to isolate tagged nuclei in mice (similar to INTACT; [Deal R.B. and Henikoff S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 18,1030-1040. (2010)]) and used it to characterize genome-wide patterns of transcription, DNA methylation, and chromatin accessibility in 3 major neuron classes of the neocortex (excitatory pyramidal neurons, parvalbumin (PV)-positive GABAergic interneurons, and vasoactive intestinal peptide (VIP)-positive GABAergic interneurons). By combining cell purification and integrative analysis, our findings relate the phenotypic and functional complexity of neocortical neurons to their underlying transcriptional and epigenetic diversity. RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq for histone modifications using INTACT-purified nuclei from the mouse neocortex

2015-06-17 | E-GEOD-63137 | biostudies-arrayexpress

AA Effector CD8 T cell profiling

Project description:Flow sorted CD3+CD8+CD44+CXCR3+NKG2D+ lymph node cells from C3H/HeJ mice with alopecia were flow sorted and profiled in relation to CD3+CD8+CD44+CXCR3+NKG2D- lymph node cells from the same host Cell populations were sorted from three separate mice

2014-08-17 | E-GEOD-45657 | biostudies-arrayexpress

Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome

Project description:This study uses Whole Transcriptome Shotgun Sequencing (RNA-Seq) data to interrogate the developmental dynamics of the C57BL/6 mouse liver transcriptome. We analyze gene expression patterns in the developing mouse liver over 12 distinct time points from late embryonic stage (2 days before birth) to maturity (60 days after birth). Biological functions deemed significant at different developmental stages are identified and their leverage is mapped over time. Upstream regulators modulating these gene expression patterns are determined and their regulatory networks are described along with putative transcriptional modules associated with gene regulation. Several genes that were alternatively spliced over time were identified. Previously uncharacterized isoforms were found for several genes. We analyze gene expression patterns in the developing mouse liver over 12 distinct time points from late embryonic stage (2 days before birth) to maturity (60 days after birth). Three replicates per time point.

2014-10-16 | E-GEOD-58827 | biostudies-arrayexpress

Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma

Project description:CD38 is a surface ectoenzyme expressed at high levels on myeloma plasma cells and is the target for the monoclonal antibodies (mAbs) daratumumab and isatuximab. CD38 density on tumor cells is an important determinant of mAb efficacy while CD38 is lost after mAb treatment. Several small molecules have been found to increase tumor surface CD38, with the goal of boosting mAb efficacy in a co-treatment strategy. Here we sought to extend our currently limited insight into CD38 surface expression by using a multi-omics approach. Genome-wide CRISPR-interference screens integrated with patient-centered epigenetic analysis confirmed known regulators of CD38, such as RARA, while revealing XBP1 and SPI1 as other key transcription factors governing surface CD38 levels. CD38 knockdown followed by cell surface proteomics demonstrated no significant remodeling of the myeloma “surfaceome” after genetically-induced loss of this antigen. Integrated transcriptome and surface proteome data confirmed high specificity of all-trans retinoic acid in upregulating CD38 in contrast to broader effects of azacytidine and panobinostat. Finally, unbiased phosphoproteomics identified inhibition of MAP kinase pathway signaling in tumor cells after daratumumab treatment. Our work provides a resource to design strategies to enhance efficacy of CD38-targeting immunotherapies in myeloma.

2021-07-29 | PXD027594 | Pride

Transcriptome analysis of renal cancer from the Cancer Genomics of the Kidney (CAGEKID) project

Project description:The incidence of renal cell carcinoma (RCC) is increasing worldwide, and its prevalence is particularly high in some parts of Central Europe. The study describes transcriptome sequencing of clear cell RCC (ccRCC), the most common form of the disease, in patients from four different European countries with contrasting disease incidence.

2014-10-29 | E-MTAB-3033 | biostudies-arrayexpress

single cell RNAseq on isolated spinal cord cells before and 3 day post tail amputation in Xenopus tropicalis tadpoles at stage NF50

Project description:The tails of stage NF50 Xenopus tropicalis tadpoles were amputated and samples were collected at 0 and 3 days post amputation. 10 spinal cords were isolated for each time point. After cell dissociation, single cell RNAseq was performed using 10X Genomics platform

2021-05-21 | E-MTAB-8839 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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