Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of gene expression associated to altered gene dosage of DeIF6 during eye development in Drosophila melanogaster

ABSTRACT: We investigated the transcriptome of the eye imaginal discs and retinae in wild type (GMR/+) and DeIF6 overexpressing (GMR>DeIF6) flies at the third instar larva stage and pupa 40 hours after puparium formation.

INSTRUMENT(S): Illumina HiSeq 2500, Illumina HiScanSQ

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Roberta Alfieri

PROVIDER: E-MTAB-5954 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Id2a knockdown in zebrafish retina

Project description:During vertebrate retinogenesis, the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways. Moreover, there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways, which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non-autonomous role for the intrinsic HLH factor, Id2a, in regulating retinoblast proliferation and differentiation, with Id2a-deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia. Here, we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis. Id2a-deficient retinae possess elevated levels of Notch pathway component gene expression, while retinae overexpressing id2a possess reduced expression of Notch pathway component genes. Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a-deficient retinae. In addition to regulating Notch pathway activity, through an RNA-Seq and differential gene expression analysis of Id2a-deficient retinae, we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a. These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Two biological replicates for both Id2aMM and Id2aMO samples

2012-08-27 | E-GEOD-38786 | biostudies-arrayexpress

Transcription profiling of Drosophila eye antennal imaginal disc expressing either activated Ras or secreted Spitz

Project description:We have used microarrays to identify genes expressed and required for the second mitotic wave (SMW) during eye development. Eye discs expressing Spitz under the control of GMR Gal4 have no SMW as Spitz promotes G1 arrest, ectopic differentiation also occures. To control for the ectopic differentiation, Spi expressing eye antennal discs were compared to eye antennal discs expressing activated RasV12. In discs expresseding RasV12 under the control of GMRGal4 the SMW takes place normally prior to any ectopic differentiation. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Experiment Overall Design: Drosophila eye antennal imaginal discs expressing either UAS RasV12 or UAS Spi under the control of GMRGal4 were dissected from 3rd instar larvae for RNA extraction and hybridization on Affymetrix microarrays.

2008-06-14 | E-GEOD-6300 | biostudies-arrayexpress

Ets-domain transcription factor Ets21c and nuclear receptor Ftz-F1 are novel effectors of JNK promoting tumor malignancy

Project description:Cancer represents a complex family of diseases, characterized by the uncontrolled malignant growth of a particular cell type and by metastatic dissemination of these transformed cells to secondary sites. The hallmark tumor features emerge as a result of aberrant cellular signaling and pathological gene expression driven by cooperating genetic lesions. Being the convergence points of signaling pathways, transcription factors play crucial roles in cancer. Here, we define a transcription factor network that triggers an abnormal gene expression program promoting malignancy of clonal tumors, generated in Drosophila imaginal disc epithelium by overexpressing oncogenic Ras (RasV12) in a background lacking the tumor suppressor gene scribble (scrib1). We show that the nuclear receptor Ftz-F1 and the ETS-domain transcription factor Ets21c are upregulated in the rasV12scrib1 tumors in response to activated Jun-N-terminal kinase (JNK) signaling. Depletion of either Ftz-F1 or Ets21c improves viability of Drosophila larvae suffering from tumors, and this effect can be further enhanced by simultaneous removal of the Jun-dimerizing partner Fos. We identified Fos as a key mediator of JNK-induced differentiation defects and further show that Ftz-F1 and Fos are required for tumor invasiveness. However, only Ets21c can efficiently substitute for JNK and cooperate with RasV12 to induce invasive tumors that recapitulate hallmarks of malignant rasV12scrib1 tumors including elevated matrix metalloprotease (MMP1) and insulin-like peptide 8 (Dilp8) expression. In conclusion, our study provides functional evidence for a network of cooperating transcription factor that dictates target gene expression and promotes tumor phenotypes in response to aberrant JNK signaling. 20 samples analyzed, 4 control samples

2015-11-04 | E-GEOD-65261 | biostudies-arrayexpress

Targeted DamID-seq of the Drosophila carpet glia

Project description:Identification of POLII binding to profile the expressed genes in the carpet glia

2019-03-22 | E-MTAB-7475 | biostudies-arrayexpress

Identification of lineage-specific cis-regulatory modules associated with variation in transcription factor binding and chromatin activity using Ornstein-Uhlenbeck models

Project description:Whole-chromatin profile (FAIRE-seq) in three Drosophila species (D. melanogaster, D. pseudoobscura and D. virilis) in eye-antennal imaginal discs at the stage of third instar wandering larvae. By the use of Ornstein-Uhlenbeck methods, we assess the evolutionary forces acting on regulatory elements (cis-level) on chromatin activity across Drosophila eye-antennal imaginal discs at the stage of third instar larvae.

2015-06-17 | E-GEOD-59706 | biostudies-arrayexpress

Transcription profiling of chicken retinal gene expression during imposed myopic defocus

Project description:The retina plays an important regulatory role in ocular growth. To screen for new retinal candidate genes that could be involved in the inhibition of ocular growth, we used chick microarrays to analyze the changes in retinal mRNA expression after myopic defocus was imposed by positive lens-wear. Chicks were raised under a 12h-light/12h-dark cycle (light-onset: 8:00 am and light-offset: 8:00 pm) with unrestricted access to water and food. On the day prior to the experiment, velcro rings were glued to the feathers around the eye under diethylether anaesthesia. Four male white leghorn chicks, aged 9 days, wore +6.9D spectacle lenses over both eyes for 24 hours. Four untreated age-matched male chicks from the same batch served as controls. After decapitation of the chicks, the eyes were enucleated and the retina was prepared. The retinae from both eyes of each chick were pooled for RNA isolation. Experiment Overall Design: Four samples each: Retina of both eyes of +6.9 diopter lens-treated chicks (plus_lens), Retina of both eyes of untreated control chicks (control)

2008-11-04 | E-GEOD-11439 | biostudies-arrayexpress

Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies

Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.

2016-10-10 | PXD004039 | Pride

Mouse retina LC-MSMS - Diurnal expression of proteins in the retina of the blind cone-rod homeobox (Crx(-/-) ) mouse and the 129/Sv mouse: a proteomic study

Project description:To investigate the role of the circadian clock of the photoreceptor cells in regulation of retinal protein rhythms, we have analyzed diurnal protein expression in the photoreceptor-deficient cone-rod homeobox knock out mouse (Crx-/-). Retinal homogenates of 129/sv and Crx-/- mice were analysed by 2D-PAGE. Differentially expressed spots were in-gel digested with trypsin and identified by LC-MS/MS. Data were used to search the Swiss-Prot protein database.

2017-04-04 | PXD005556 | Pride

Profling of the Drosophila melanogaster neuronal microRNA transcriptome by small RNA deep sequencing

Project description:microRNAs (miRNAs) are a class of small non-coding RNAs involved in the coordination and/or fine-tuning of gene expression. As such, miRNAs are thought to be critical cis-acting regulatory factors that control a wide range of physiological processes in the brain. The datasets presented here represent the miRNA transcriptome of the adult and larval Drosophila melanogaster CNS as determined by small RNA deep sequencing (RNA-Seq). They were derived from adult and larval samples explanted from the animal that contain minimal extraneous (non-neuronal) tissues. Here we present a concise summary of our profiling results as well as the original sequencing data. We identify many miRNAs that are expressed at equal levels in both tissues and several that are significantly enriched in the larval and adult brain. Some of these belong to miRNA families with conserved members in mammals. These datasets should provide a good starting point for others interested in characterizing miRNAs with putative functions in Drosophila neurons. The datasets presented here represent the miRNA transcriptome of the adult and larval Drosophila melanogaster CNS as determined by small RNA deep sequencing (RNA-Seq).

2016-05-15 | E-GEOD-57687 | biostudies-arrayexpress

An ectopic network of transcription factors regulated by Hippo signaling drives growth and invasion of a malignant tumor model

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-06-10 | E-GEOD-71354 | biostudies-arrayexpress