Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of wild type and mutant Drosophila flies with a deletion of the gene CG16717 (dMPPED)

ABSTRACT: Flies deficient in the gene CG16716 were created and showed a reduced life span when compared to wild type w1118 flies. Flies were harvested on day 35 (both wild type and mutant flies), RNA prepared and subjected to RNA-seq.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Sandhya Visweswariah

PROVIDER: E-MTAB-9081 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq on Illumina platform of Drosophila DrosDel deficiency lines

Project description:RNA-Seq reads of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Illumina platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #_platform. We sequenced mRNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies).

2012-04-03 | E-GEOD-31549 | biostudies-arrayexpress

RNA-Seq on SOLiD platform of DrosDel deficiency and w1118 flies

Project description:RNA-Seq reads of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the SOLiD platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #_platform_technical replicate. We sequenced mRNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies). The same sample was sequenced across two flow cells on the SOLiD platform.

2012-04-03 | E-GEOD-31401 | biostudies-arrayexpress

RNA-Seq of head tissue from Drosophila melanogaster Wild Type and Adar5G1dAdar-/- mutant

Project description:Purpose: Validation of Drosophila A-to-I editing sites Methods: We collected heads of 5 day old male dAdar-/- mutant (y, Adar5G1, w)26 and wild type (w1118) flies. Poly(A)+ RNA was used to prepare RNA-seq libraries which were subsequently sequenced single-end by an Illumina GAII Results:We builded a framework to identify RNA editing events using RNA-seq data alone in Drosophila. To validate whether the identified A-to-G sites were bona fide A-to-I editing events, we performed RNA-seq for the D.melanogaster wild-type strain (w1118) and for the Adar5G1 null mutant that eliminates RNA editing. We found that our method achieved high accuracy; 98.2% of all A-to-G sites showed only adenosine in the Adar5G1 sample Conclusions: We anticipate that our method will be very effective in the future to identify RNA editing events in different species. mRNA profiles of heads of 5 day old male dAdar-/- mutant (y, Adar5G1, w)26 and wild type (w1118) flies

2012-12-20 | E-GEOD-42815 | biostudies-arrayexpress

DNA-Seq of DrosDel deficiency lines and w1118 lines

Project description:DNASeq reads from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies). Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_DNASeq_biological replicate #. We sequenced DNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies).

2012-04-03 | E-GEOD-31550 | biostudies-arrayexpress

Drosophila DrosDel deficiency and diploid control flies

Project description:GSE31386: Microarray expression analysis of Drosophila DrosDel deficiency lines GSE31401:RNA-Seq on SOLiD platform of DrosDel deficiency and w1118 flies GSE31549: RNA-Seq on Illumnia platform of DrosDel deficiency and w1118 lines GSE31550: DNA-Seq of Drosophila DrosDel deficiency and w1118 lines Refer to individual Series

2012-04-02 | E-GEOD-31407 | biostudies-arrayexpress

miRNA* loading on Ago2

Project description:In flies, microRNAs (miRNAs) are synthesized as a short imperfect duplex, where the miRNA is paired to another small RNA, dubbed the "miRNA*". Usually, miRNA*s are degraded in the last steps of miRNA maturation, but we found evidence that some of them can be loaded on the Ago2 protein. Small RNAs (18-29 nt) from fly heads (WT, ago2 mutants, dcr-2 homozygous and heterozygous mutants) were sequenced using a Solexa Genome Analyzer instrument. The ago2 cDNA library was loaded twice on the instrument, yielding two technical replicates.

2010-08-02 | E-GEOD-12462 | biostudies-arrayexpress

RNA-seq analyses of kdm5 mutant flies and wt flies under normal condition and oxidative stress

Project description:Comparing the transcriptome of wildtype and kdm5 mutant flies in normal conditions revealed a total of 4787 genes that were significantly downregulated and thus require KDM5 for their activation, and 3269 upregulated genes that are normally repressed by KDM5 (p<0.05, FDR <0.05). Because kdm5 mutants are sensitive to the oxidizer paraquat, we also carried out RNA-seq from wildtype and kdm5 mutant adults in oxidative stress conditions. Paraquat treatment of wildtype flies lead to the upregulation of 2481, and downregulation of 3103 genes adult mRNA profiles of 1-3-days old wild type (WT) and kdm5 mutant under normal condition and oxitative stress were generated by deep sequencing, using Illumina HisSeq 2000.

2015-12-22 | E-GEOD-70590 | biostudies-arrayexpress

Age and diet affect genetically separable secondary injuries that cause acute mortatlity following traumatic brain injury in Drosophia

Project description:To identify genes involved in TBI outcomes in Drosophila we compared genome-wide mRNA expression of uninjured and injured flies under both age and diet conditions. Whole male fly mRNA profiles of 0-7 day and 20-27d old Drosophila line w1118 were generated, with or without injury and under two different dietary conditions. Experiments were preformed in triplicate, using Illumina HiSeq 2500.

2016-08-20 | E-GEOD-85821 | biostudies-arrayexpress

Phospoproteome along the dorso-ventral axis of the early Drosophila embryo

Project description:The initially homogeneous epithelium of the early Drosophila embryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso-ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3399 and 3433 respectively, were differentially regulated. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway, Toll10B and serpin27aex do this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo. This repository is related to PXD046050 which represents the label-free proteome.

2024-10-01 | PXD046192 | Pride

Transcription profiling of Drosophila adults to assess the effect of LARK overexpression in CNS neurons

Project description:The goal of this study is to identify, in the head of adult flies, mRNA species whose expresson level are altered by overexpression of the Drosophila RNA-binding protein LARK in CNS neurons. Experiment Overall Design: RNA samples from adult head of the LARK overexpression flies (elav-gal4; uas-lark/+) and control flies were compared. One total RNA sample was isolated from each genotype, of which three technical replicates (repeating the labeling and hybridization processes) were generated, respectively.

2008-06-14 | E-GEOD-6420 | biostudies-arrayexpress

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