Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome expression analysis in the third-instar larval midgut of Drosophila melanogaster

ABSTRACT: Survival of insects on a substrate containing toxic substances such as plant secondary metabolites or insecticides is dependent on the metabolism or excretion of those xenobiotics. The primary sites of xenobiotic metabolism are the midgut, Malpighian tubules and fat body. In general, these organs are treated as single tissues by online databases, but several studies have shown that gene expression within subsections of the midgut is compartmentalized. In this article, RNA sequencing analysis was used to investigate whole-genome expression in subsections of the third-instar larval midgut. The results support functional diversification in subsections of the midgut. Analysis of the expression of gene families that are implicated in the metabolism of xenobiotics suggests that metabolism may not be uniform along the midgut. These data provide a starting point for investigating gene expression and xenobiotic metabolism in the larval midgut.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE32329 | GEO | 2014/09/20

SECONDARY ACCESSION(S): PRJNA147279

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Whole genome expression analysis in the third-instar larval midgut of Drosophila melanogaster

Project description:Survival of insects on a substrate containing toxic substances such as plant secondary metabolites or insecticides is dependent on the metabolism or excretion of those xenobiotics. The primary sites of xenobiotic metabolism are the midgut, Malpighian tubules and fat body. In general, these organs are treated as single tissues by online databases, but several studies have shown that gene expression within subsections of the midgut is compartmentalized. In this article, RNA sequencing analysis was used to investigate whole-genome expression in subsections of the third-instar larval midgut. The results support functional diversification in subsections of the midgut. Analysis of the expression of gene families that are implicated in the metabolism of xenobiotics suggests that metabolism may not be uniform along the midgut. These data provide a starting point for investigating gene expression and xenobiotic metabolism in the larval midgut. Examination of expression in eight samples corresponding to compartments of gene expression in the midgut

2014-09-20 | E-GEOD-32329 | biostudies-arrayexpress

Transcription profiling by array of Yellow Fever mosquito, Aedes aegypti, larval midgut modifications associated with Bti resistance

Project description:This study aimed at comparing gene transcription using microarrays and protein expression using 2D-DIGE between an Aedes aegypti insecticide-resistant strain (LiTOX) selected for 28 generations at the larval stage with field-collected leaf litter containing persistent Bacillus thuringiensis var. israelensis (Bti) toxins and the parental strain (Bora-Bora) susceptible to all insecticides. We focused on the tissue where the mode of action of the insecticide takes place: the midgut of the larvae.

2012-06-01 | E-MTAB-1094 | biostudies-arrayexpress

Manduca sexta differential gene expression, male & female antenna, larval midgut

Project description:To allow estimation of the complexity of the antennal transcriptome between sexes as well as in comparison with a non-antennal tissue, microarrays were designed based on an assembly of new 454 sequence data from the antenna and publicly available data including 454 data from the larval midgut. The microarrays were hybridized with samples generated from the repsecitve tissues from 3 (antenna) and 5 (midgut) animals per sample, with four independent samples per sex (antenna) and tissue (midgut).

2011-03-01 | GSE27470 | GEO

A cell atlas of the adult Drosophila midgut

Project description:Drosophila guts were dissociated to single cells as previously described (Dutta et al., 2015) with a few modifications. Guts were dissected from 7-day old adult esg-sfGFP/+, pros- Gal4>RFP/+ females. After pulling out the gut, the crop and midgut/hindgut junction (where the Malpighian tubules branch out of the gut) and Malpighian tubules were removed. Five flies at a time were dissected and immediately transferred into cold PBS containing 1% BSA to avoid exposing the midgut tissue to room temperature for a long period of time. Once 40 guts were dissected, they were transferred to a dissection plate and chopped into small pieces using a razor blade. These small fragments were immediately transferred to an eppendorf tube containing 400 ul of 1 mg/ml elastase/PBS solution (Sigma E0258) and incubated on a shaker at 27 ̊C for 30 min. 1% of BSA in PBS (final concentration) was used to stop the digestion reaction and prevent cells from aggregating. The cell suspension was passed through 100 um and then a 40 um cell strainer and loaded on the top of Optiprep with density gradient 1.12 g/ml. Viable cells were isolated from the top layer of the sample after centrifugation at 800xg for 20 min. Cell viability and number were assessed by 0.4% trypan blue and hemocytometer.

2019-12-19 | GSE120537 | GEO

Expression profile of third instar larval fat body and midgut tissues

2010-11-02 | GSE25025 | GEO

Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning

Project description:The identification of xenobiotics through nontargeted analysis is a vital step in understanding human exposure, however metabolism, excretion, and co-existence with other endogenous molecules in the metabolome greatly complicate their measurements. Xenobiotics are therefore commonly undetected and exist as part of the dark metabolome. While mass spectrometry (MS)-based platforms are commonly used in metabolomic measurements, deconvoluting endogenous metabolites and xenobiotics is often limited by a lack of xenobiotic parent and metabolite standards as well as the numerous isomers possible for each m/z feature. Here we evaluated the ability of ion mobility spectrometry (IMS) and mass defect filtering techniques to narrow large metabolomic feature lists to xenobiotics of interest. Due to the lack of IMS collision cross section (CCS) values for per- and polyfluoroalkyl substances (PFAS), we initially evaluated 87 PFAS standards with IMS-MS to develop a PFAS CCS library. The detected PFAS CCS and m/z values were then compared to other biomolecule and xenobiotic classes, illustrating clear differentiation between the biomolecules and the halogenated xenobiotics. To address the lack of xenobiotic standards, machine learning was then utilized to predict CCS values. Ultimately, a xenobiotic selection workflow combining experimental and theoretical CCS values and mass defect filtering was employed to evaluate PFAS features in NIST human serum. This workflow reduced the 2,423 LC-IMS-MS features to 98 possible PFAS, and 23 were identified using homologous series information.

2021-10-11 | MSV000088215 | MassIVE

ADME gene variants in multiple myeloma susceptibility

Project description:The metabolism of xenobiotics is regulated by phase I and II enzymes, and by transporters encoded by the absorption, distribution, metabolism, and excretion (ADME) genes. It is known that the activity of these proteins is influenced by the presence of polymorphic variants in the corresponding gene that can account for the inter-individual variability in both xenobiotic response/toxicity and disease predisposition. Exposure to pesticides and toxic substances, many of which are substrates of ADME-associated proteins, has been demonstrated to increase the risk of Multiple Myeloma (MM). To investigate the inter-individual variability of ADME genes as a risk factor for MM risk, we compared DMET Plus genotyping data from 65 MM patients with 59 CEU Hapmap controls (GPL17860).

2021-11-03 | GSE187009 | GEO

Expression profile of third instar larval fat body and midgut tissues

Project description:We use mRNA-seq to transcriptionally profile larval fat body and midgut tissues from Drosophila third instar larvae. These data provide insights into tissue physiology and can be used to identify tissue specific transcripts. Fat bodies from wandering third instar larvae were dissected from ~50 male larvae and gonads were removed to eliminate contaminating transctips from the gonads. Larval midguts were dissected from ~50 wandering third instar larvae. Larval tissues were removed to Graces unsupplemented medium on ice prior to RNA extraction with TRIzol reagent. mRNA-seq samples were prepared from 5ug of total RNA and subject to Illumina based sequencing.

2010-11-02 | E-GEOD-25025 | biostudies-arrayexpress

Midgut metamorphosis timecourse

Project description:A midgut reference sample is compared to midgut samples taken at various stages before (18h, 4h), at (0h), and after (2h, 3h, 4h, 5h, 6h, 8h, 10h, 12h) puparium formation. Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development Keywords: other

2003-07-23 | GSE543 | GEO

Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multi-algorithm Pipeline

Project description:Plutella xylostella is the major cosmopolitan pest of brassica and other crucifer crops, the larval midgut of which is a dynamic organ that interfaces with a divers earray of physiological and toxicological processes. The draft sequence of the P.xylostella genome was recently released, but its annotation remains challenging because of the low coverage of this branch of life.Peptide sequencing by computational assignment of tandem mass spectra to a database of putative protein sequences provides an independent approach to confirm or refute protein prediction, which has been termed proteogenomics. In this study we carried out an in-depth proteogenomic analysis using shotgun HPLC-ESI-MS/MS approach with a multi-algorithme pipeline to complement genome annotation in the P.xylostella larval midgut.

2015-10-12 | PXD002028 | 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