Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq experiment of Drosophila melanogaster larvae reared on Aspergillus nidulans infested breeding substrate

ABSTRACT: Drosophila melanogaster larvae and filamentous fungi both utilise organic material. Here they compete for resources. Filamentous fungi can defend themselves and their substrate from predation respectively competition by the production and excretion of secondary metabolites, including substances with antibiotic and insecticidal properties. To analyse the traits that enables D. melanogaster larvae to reduce the harmful effects of fungal secondary metabolites and to develop on fungal infested substrate we confronted larvae with a toxin-producing wild type of Aspergillus nidulans, with a toxin-production-impaired mutant strain of A. nidulans, and with sterigmatocystin, a highly toxic metabolite of A. nidulans. Early first instar larvae were transferred to breeding substrate inhabited by fungal colonies respectively inoculated with the purified mycotoxin or controls. After 3, 6, 12, and 24 hours of confrontation larvae were collected and samples prepared for whole transcriptome shotgun sequencing.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Monika Trienens

PROVIDER: E-MTAB-5344 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Drosophila melanogaster selection lines confronted with Aspergillus nidulans

Project description:Experimental evolution was conducted using Drosophila melanogaster populations that developed as larvae on breeding substrate that was infested with Aspergillus nidulans wild type, A. nidulans toxin-impaired mutant strain delta-laeA, the mycotoxin sterigmatocystin, or on fungi and toxin free substrate. Overall population were reared under these conditions for 11 generations, where after each confrontation generation one relaxation generation (fungi and toxin free breeding substrate) was conducted. Nine generations after the last selection treatment, first instar larvae were confronted with 3 days old A. nidulans wild type colonies or control conditions. 24 hours after confrontation start larvae were collected. For each biological replicate 52 larvae were collected from 4 independent confrontation units, balanced design. Three populations per selection regime were conducted, resulting in: 2 conditions x 4 selection regimes x 3 biological replicates (equal to fly population) = 24 samples. Selection regimes: sCO= control; sWT= A. nidulans wild type; sLA= A. nidulans mutant strain; sST= Sterigmatocystin. confrontation condition: cCO= control; cWT= A. nidulans wild type.

2020-05-09 | E-MTAB-9011 | biostudies-arrayexpress

Transcriptome analysis of N,C and P limitations in S. coelicolor

Project description:A genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon

2011-05-01 | E-MAXD-59 | biostudies-arrayexpress

TCC in pluripotent and differentiated cells

Project description:Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked. Recently CTCF anchored loops have been described as major features of chromatin organisation. However, the dynamics and role for these structures in differentiation is unknown. We used Tethered Chromatin Conformation Capture (TCC) to assess for the dynamics of CTCF-anchor loop formation upon differentiation of mouse embryonic stem cells (ESC) and neural stem cells (NSC).

2018-11-08 | E-MTAB-4870 | biostudies-arrayexpress

the Interaction Proteome of Ribosomal 40S Components PNO1 and NOB1 Using TurboID Proximity Labeling Technology

Project description:Background: The ribosome assembly factors PNO1 and NOB1 play crucial roles in the maturation of the 40S ribosomal small subunit. TurboID is an efficient biotin ligase that can biotinylate proteins in proximity to the target protein and is widely used to study complex biological processes within cells.Here, we utilized this technology to investigate the complex interaction network of PNO1 and NOB1 within cells.

2024-06-08 | PXD052825 | Pride

Mouse embryonic RNA-seq

Project description:The study was aimed at interrogating the early stages of blood cell development within the embryo. Blood develops from mesoderm, which is specified at gastrulation. We therefore sorted cells from mouse embryos between E6.5 and E7.75 to capture gastrulation and the emergence of mesoderm, followed by specificiation of the first mature blood cells.

2016-07-08 | E-MTAB-4079 | biostudies-arrayexpress

Transcriptional time course of the response to oxidative stress in Drosophila

Project description:We exposed flies to acute oxidative stress-inducing concentrations of paraquat and menadione sodium bisulfite and corresponding controls and obtained whole-genome transcript profiles at three time points (30 minutes, 4 hours and 10 hours) during exposure.

2014-08-21 | E-MTAB-1291 | biostudies-arrayexpress

Dynamic alterations of 3D chromatin structure during differentiation

Project description:Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked at long-range via positioning of loci to transcriptionally permissive (euchromatin) or repressive (heterochromatin) environments and at short-range by connecting cis regulatory elements such as promoters and enhancers. However, the dynamics of these processes during cell differentiation still remains unclear. We used Tethered Chromatin Conformation Capture (TCC) to compare the three dimensional chromatin structure of mouse embryonic stem cells (ESC) and neural stem cells (NSC) which we directly derived from the ESC.

2019-08-27 | E-MTAB-2063 | biostudies-arrayexpress

Genome-wide binding of Sd and Yki in imaginal discs

Project description:The transcription cofactor Yki drives growth and proliferation in part by controlling mitochondrial network formation. To determine if Yki and Sd are directly bound to DNA corresponding to mitochondrial genes, we used chromatin immunoprecipitation and whole genome tiling arrays (ChIP-chip) to identify regions bound by these factors in eye-antenna and wing imaginal discs. The supplementary .bed files contain all Yki or Sd binding sites (called at 5% FDR) in wing or eye-antenna imaginal discs, as well as shared Sd+Yki sites and associated target genes. Wing or eye-antenna imaginal discs ChIPped for Yki or Sd-GFP vs. input DNA from corresponding imaginal discs.

2012-10-03 | E-GEOD-26678 | biostudies-arrayexpress

Genome-wide binding of Ubx and Hth in 3rd thoracic imaginal discs

Project description: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. All Hox genes, including Ubx, encode homeodomain containing transcription factors, raising the question of what target genes Ubx regulates to generate these adult structures. To address this question, we carried out whole genome ChIP-chip studies to identify all of the Ubx bound regions in the haltere and T3 leg imaginal discs, which are the precursors to these adult structures. In addition, we used ChIP-chip to identify the sites bound by the Hox cofactor, Homothorax (Hth). This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This dataset was generated in collaboration with Richard S. Mann at Columbia University. It contains ChIP-chip data on Affymetrix Drosophila Tiling 2.0R arrays for multiple transcription factor antibodies in multiple Drosophila tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Haltere or leg imaginal discs ChIPped for Ubx or Hth vs. input DNA from corresponding imaginal discs. For each combination of tissue and antibody, ChIP experiments have been performed and hybridized on Affymetrix Drosophila Tiling 2.0R arrays. At least 3 biological replicates for the ChIP sample have been hybridized.

2011-01-21 | E-GEOD-26793 | biostudies-arrayexpress

Prednisolone alters decidualization and affects decidual-trophoblast interactions

Project description:Identification of cellular proteins in human endometrial stromal fibroblasts decidualized for 13 days in vitro. Fibroblasts were cultured under normal culture conditions (5% CO2 in 2% charcoal stripped FBS) and treated with prednisolone (0.5ug/ml) or vehicle control (DMSO) every 48-72h for 13 days

2021-04-27 | PXD020543 | Pride

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