Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression profiling of the Global Diversity Lines

ABSTRACT: The Global Diversity lines are a resource collection of 87 strains of Drosophila melanogaster (Grenier JK et al 2015. PMID 25673134). In this experiment, whole adult flies from the Global Diversity Lines (87 inbred lines derived from natural populations) were profiled using a spotted-oligo microarray to determine natural variation in gene expression patterns.

INSTRUMENT(S): GenePix 4000B

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Jennifer Grenier

PROVIDER: E-MTAB-4580 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

eQTL mapping in 57 F1 diversity lines of Arabidopsis thaliana

Project description:eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions 57 F1 lines without replicates, the 5th or 6th true leaf

2011-03-01 | E-GEOD-23912 | biostudies-arrayexpress

IRF-5 and IRF-8 govern the response of Human Plasmacytoid Dendritic Cells following TLR9 ligation

Project description:Synthetic oligonucleotides (ODNs) containing CpG motifs stimulate human plasmacytoid dendritic cells (pDCs) to produce type-1 interferons (IFN) and pro-inflammatory cytokines. Previous studies demonstrated that interferon regulatory factors (IRFs) played a central role in mediating CpG-induced pDC activation. This work explores the inverse effects of IRF-5 and IRF-8 on CpG dependent gene expression. Results from RNA interference and microarray studies indicate that IRF-5 up-regulates TLR9-driven gene expression whereas IRF-8 down-regulates the same genes. Several findings support the conclusion that IRF-8 inhibits TLR9 dependent gene expression by directly blocking the activity of IRF-5. First, the inhibitory activity of IRF-8 is only observed when IRF-5 is present. Second, proximity ligation analysis shows that IRF-8 and IRF-5 co-localize within the cytoplasm of resting human pDC and co-translocate to the nucleus after CpG stimulation. Taken together, these findings suggest that two transcription factors with opposing functions control TLR9 signaling in human pDCs. CAL-1 cells were transfected with siRNA targeting IRF-5 (IRF-5si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with siRNA targeting IRF-8 (IRF-8si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with control siRNA (Contsi) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats).

2016-06-01 | E-GEOD-70429 | biostudies-arrayexpress

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)

Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. MethylC-seq from naturally-occurring Arabidopsis accessions

2013-03-05 | E-GEOD-43857 | biostudies-arrayexpress

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)

2013-03-05 | GSE43857 | GEO

eQTL mapping in 57 F1 diversity lines of Arabidopsis thaliana

Project description:eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions

2011-03-01 | GSE23912 | GEO

Combinatorial Control of RBP-jk and EBF1 Chromosome Occupancy induced by viral co-activator EBNA2 [ChIP-seq]

Project description:Gene expression programs depend on sequence-specific DNA binding transcription factors, but the mechanisms that control the selective binding of these factors in a chromosomal and genomic context remain enigmatic. Here, we show that two master regulators of B-cell fate, namely EBF1 and RBP-jk, show variable genome-wide chromosome distribution in two related B-lymphocyte lines carrying different forms of Epstein-Barr Virus (EBV) latency. The latency-type specific EBV-encoded EBNA2 colocalized with RBP-jk and EBF1 at induced binding sites. Colocalization of EBF1, RBP-jk, and EBNA2 correlated with transcriptional activation. Conditional expression or repression of EBNA2 lead to a rapid alteration in RBP-jk and EBF1 binding. Biochemical and shRNA depletion studies provide evidence for cooperative assembly at co-occupied sites. These findings reveal that non-DNA binding cofactors can facilitate combinatorial interactions to induce new patterns of transcription factor occupancy and gene programming Examination of EBNA2/EBF1/EBP-jk binding in MutuI and LCL cell lines

2015-12-16 | E-GEOD-75503 | biostudies-arrayexpress

microRNA and mRNA gene expression signature in JK and JinB8 cell lines [mRNA]

Project description:microRNA and mRNA gene expression signature in JK and JinB8 cell lines.

2019-09-30 | GSE132644 | GEO

microRNA and mRNA gene expression signature in JK and JinB8 cell lines [miRNA]

Project description:microRNA and mRNA gene expression signature in JK and JinB8 cell lines.

2019-09-30 | GSE132645 | GEO

A Pitx2-miRNA pathway modulates cell proliferation in myoblasts and skeletal-muscle satellite cells and promotes their commitment to a myogenic cell fate.

Project description:The acquisition of a proliferating cell status from a quiescent state as well as the shift between proliferation and differentiation are key developmental steps in skeletal-muscle stem cells (satellite cells) to provide proper muscle regeneration. However, how satellite-cell proliferation is regulated, though, is not fully understood. Here, we report that the c-isoform of the transcription factor Pitx2 increases cell proliferation in myoblasts by down-regulating the miRNAs miR-15b, miR-23b, miR-106b, and miR-503. This Pitx2c-miRNA pathway also regulates cell proliferation in early-activated satellite cells, enhancing the Myf5+ satellite cells and thereby promoting their commitment to a myogenic cell fate. This study reveals unknown functions of several miRNAs in myoblast and satellite-cell behaviour and thus may have future applications in regenerative medicine. mirVana microarrays (Ambion) were used to profile microRNA signature at different Pitx2 overexpression conditions, namely two different doses (4 and 8 µg CMV-Pitx2c plasmid, respectively) after 24 hours of transfection in SOL8 skeletal myogenic cells. 20 µg of total RNA was used to hybridize two distinct microRNA microarrays on each condition analyzed.

2015-06-10 | E-GEOD-53943 | biostudies-arrayexpress

The natural diversity of the yeast proteome links aneuploidy tolerance to protein turnover

Project description:Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions, and allows assessment of the generalizability of laboratory findings. One notable discovery made in Saccharomyces cerevisiae natural isolates is frequent (~20%) aneuploidy – an imbalance in chromosome copy numbers – that appears to contradict the significant fitness costs and transient nature reported for lab-engineered aneuploids. Here, we generated a proteomic resource and merged it with genomic and transcriptomic data for 796 euploid and aneuploid natural isolates. We found that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins, especially protein complex subunits, show reduced expression, yet the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage-compensated, with average protein levels being shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and demonstrates the utility of exploiting the natural diversity of species to reach generalizable molecular insights into complex biological processes. This resource provides the SILAC dataset from this work.

2024-03-13 | PXD048219 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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