Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling of Drosophila melanogaster photoreceptors following nuclei affinity enrichment

ABSTRACT: Purpose: The goal of this study was to globally characterize the transcript levels of genes in Drosophila photoreceptor neurons. Using transcriptome profiling of isolated photoreceptor nuclei from day 10 flies, we identified genes with enriched or reduced transcript levels post nuclei isolation relative to the starting pre-isolation material (whole head RNA extracts).

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE93128 | GEO | 2017/11/10

SECONDARY ACCESSION(S): PRJNA360105

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptional profiling of aged Drosophila photoreceptors

Project description:Purpose: The goal of this study was to globally characterize the transcript levels of genes in Drosophila photoreceptor neurons during aging. Using transcriptome profiling of isolated photoreceptor nuclei we analyzed the changes in gene expression that occur during aging over 5 time-points from 10 to 40 days post-eclosion and identified sets of genes with both up-regulated and down-regulated expression.

2017-11-10 | GSE83431 | GEO

Transcriptional profiling of Drosophila photoreceptors in response to blue light

Project description:Purpose: The goal of this study was to characterize the transcript levels of genes in Drosophila photoreceptor neurons in response to blue light. Using transcriptome profiling of isolated photoreceptor nuclei, we analyzed the changes in gene expression that occur in response to 3h of blue light exposure at 1 or 6 days post-eclosion. We identified sets of genes with both up-regulated and down-regulated expression in response to blue light at either age.

2018-06-20 | GSE106820 | GEO

INTACT vs. FANS for cell-type-specific nuclei isolation: A comprehensive qualitative and quantitative comparison

Project description:In this study we used transgenic mouse model to comapre two isolation techniques INTACT and FANS for the isolation of activated neuronal nuclei. Comparison is perfomed on multiple levels like isolation efficiency, membrane integrity, transcriptional and epigenetic state using RNA-seq and ATAC-seq

2021-01-28 | GSE165644 | GEO

NKX2-2 based nuclei sorting on human archival pancreas enables the enrichment of islet endocrine populations for single nucleus RNA sequencing

Project description:Current approaches to profile the single-cell transcriptomics of human pancreatic endocrine cells almost exclusively rely on freshly isolated islets. However, human islets are limited in availability. Furthermore, the extensive processing steps during islet isolation and subsequent single cell dissociation might alter gene expressions. In this work, we cross-compared five nuclei isolation protocols and selected the citric acid method as the best strategy to isolate nuclei with high RNA integrity and low cytoplasmic contamination from human pancreata. We innovated fluorescence-activated nuclei sorting (FANS) based on the positive signal of NKX2-2 antibody to enrich for nuclei of the endocrine population from the entire nuclei pool of the pancreas. Our sample preparation procedure generated high-quality single-nucleus gene-expression libraries while preserving the endocrine population diversity. We observed comparable endocrine cellular composition and cell type signature gene expression between our snRNA-seq libraries and conventional scRNA-seq libraries generated with live cells from freshly isolated human islets. Our work fills a technological gap and helps to unleash archival pancreatic tissue for molecular profiling targeting the endocrine population. We expect that our protocol can be used to enrich nuclei for transcriptomics study from various populations in the pancreas and in different organs/tissues.

2024-04-01 | GSE252614 | GEO

Gene expression profiling in ninaE wild type and ninaE G69D/+ Drosophila photoreceptors

Project description:Cell type specific gene expression profiling was performed with adult Drosophila photoreceptors. Two genotypes were compared: ninaE wild type control and ninaEG69D/+ mutants that have chronic endoplasmic reticulum stress. To specifically isolate RNAs from these cell types, we drove nuclear envelope-localized EGFP::Msp300KASH expression with the photoreceptor specific Rh1-Gal4 driver. Anti-GFP beads were used to isolate the nuclei from those adult fly photoreceptor cells. Novaseq was used to perform RNA-seq.

2021-10-02 | GSE185134 | GEO

Genome-Wide CRX Binding Sites in adult mouse photoreceptors

Project description:CRX is a key transcript factor for photoreceptor development and homeostasis. We have characterized the CRX-dependent cis-regulatory network by ChIP-chip analysis of 2 month old BL/6 mouse retinas using Affymetrix Mouse Promoter 1.0 arrays

2010-08-17 | GSE23567 | GEO

Deciphering the cis-regulatory architecture of mammalian photoreceptors

Project description:In order to define the genomic targets of Crx, we carried out Crx chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) of eight-week-old mouse retinas using the Solexa platform. Sequence reads were mapped to the genome and 'peaks' were identified. These data were subjected to extensive bioinformatic analysis. In addition, selected peaks were experimentally tested for cis-regulatory activity by electroporation as promoter-reporter fusions into living mouse retinas. Over 5,000 Crx-bound regions (CBRs) were identified throughout the mouse genome. Many of these clusters of CBRs occur specifically around photoreceptor genes. In fact, Crx directly regulates the majority of known photoreceptor transcription factors as well as most known photoreceptor disease genes. Cis-regulatory analysis revealed that individual CBRs contribute in a combinatorial fashion to the overall activity of the gene they control. In addition, multiple Crx-binding sites within CBRs cooperatively interact via precise spacing rules to generate optimal levels of transcription. Crx ChIP-Seq analysis of C57BL/6 and Nrl-/- retinas. IgG ChIP-Seq was performed as a control. 1-2 replicates each.

2010-06-24 | E-GEOD-20012 | biostudies-arrayexpress

Drosophila melanogaster

Project description:Isolation of mRNA from fly photoreceptor cells by mRNA tagging

| PRJNA90587 | ENA

RNA profile of nuclei isolated from neurons coexpressing VAChT and VGlut or VAChT and VGAT

Project description:The concept of neurotransmitter identity, once considered singular and immutable for mature neurons, has been broadened by the recognition that many neurons release multiple neuro-active substances. In order to demonstrate the extent of neurotransmitter co-expression, we labelled neuronal nuclei with UNC84-GFP using VAChT and either Vglut or VGAT split-GAL4s and isolated them with the isolation of nuclei tagged in specific ell types (INTACT) method From the isolated nuclei, we isolated and sequenced Poly(A) RNA and examined the relative expression levels of glutamatergic, GABAergic, or cholinergic genes in each population.

2022-12-31 | GSE221859 | GEO

An optimized RNA-seq workflow for isolating single nuclei from clinical biopsies

Project description:We developed an optimized protocol for nuclei isolation from small core needle biosies taken from both healthy and diseased human kidney samples

2022-06-22 | GSE195719 | 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