Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Splicing_Arrays_1

ABSTRACT: In this work, we have studied four closely related members of the five known Drosophila hnRNP A/B family, hrp36, hrp38, hrp40, and hrp48. Using splicing-sensitive microarrays, between 200 and 300 genes were detected as specifically regulated by each individual hrp protein following down regulation of the protein expression level by RNAi-mediated knock-down. Keywords: Genetic modification Each individual protein (four total) were individually knock-down. RNA from biological triplicates were isolated 4 days after the initial treatment. A non-specific RNAi control was performed and the RNA isolated from multiple replicates were pooled and used as control sample in the microarray.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Marco Blanchette

PROVIDER: E-GEOD-13943 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members.

Blanchette Marco M Green Richard E RE MacArthur Stewart S Brooks Angela N AN Brenner Steven E SE Eisen Michael B MB Rio Donald C DC

Molecular cell 20090201 4

Heterogeneous nuclear ribonucleoproteins (hnRNPs) have been traditionally seen as proteins packaging RNA nonspecifically into ribonucleoprotein particles (RNPs), but evidence suggests specific cellular functions on discrete target pre-mRNAs. Here we report genome-wide analysis of alternative splicing patterns regulated by four Drosophila homologs of the mammalian hnRNP A/B family (hrp36, hrp38, hrp40, and hrp48). Analysis of the global RNA-binding distributions of each protein revealed both smal ...[more]

PMID: 19250905

Similar Datasets

Splicing_Arrays_2

Project description:In this work, we have studied four closely related members of the five known Drosophila hnRNP A/B family, hrp36, hrp38, hrp40, and hrp48. Using splicing-sensitive microarrays, between 200 and 300 genes were detected as specifically regulated by each individual hrp protein following down regulation of the protein expression level by RNAi-mediated knock-down. Keywords: Genetic modification This set of arrays evaluate the off target effect of the RNAi. Two differerent non-overlapping dsRNA targeting hrp36 were used to knock down its expression. The net-expression value of each splicing junction was then extracted and compare.

2008-12-30 | E-GEOD-13944 | biostudies-arrayexpress

RNAi knockdown of NMD in D Melanogaster

Project description:Two core factors of the NMD machinery in D. melanogaster, Upf1 and Upf2, were knocked down using RNAi, as described in Rehwinkel et al. (2005) RNA, PMID: 16199763. Each of the two knockdowns were compared to mock RNAi knockdowns as described in Blanchette et al. (2005) Genes Dev, PMID: 15937219 in a dual channel experiment, using a custom splice-junction microarray design, see Blanchette et al. (2005), PMID: 15937219. The aim of the experiment was to identify which isoforms of alternatively spliced genes were affected by NMD knockdown and thereby gain insight into the NMD mechanism in Drosophila. The samples were hybridized in a dual channel setup, to custom designed Splice-Junction arrays manufactured by Agilent. A total of 6 independent knockdowns (3 Upf1 and 3 Upf2) were generated and hybridized to 6 different arrays. On each array a control sample was hybridized as well. The control sample is a pool of 3 independent mock RNAi knockdowns.

2010-05-18 | E-GEOD-13532 | biostudies-arrayexpress

Gene expression after single and dual insulator protein knock-downs in Drosophila Kc cells.

Project description:Transcriptional changes assayed with two bilogical replicates in wild type and RNAi mediated insulator knock-downs RNAi mediated insulator knock-downs cause changes in the H3K27me3 levels and spread of Topoisomerase II In order to understand the role of insulators in gene expression and regulation we used Drosophila Kc cells to knock-down single and multiple insulators in combination to assay for transcriptional changes. Two biologial replicates were prepared in independent experiments. Each cDNA samples were labeled with Cy3 dye and hybridized and scaned as per manufactures instructions at Florida State University Nimblegen facility.

2012-06-17 | E-GEOD-36944 | biostudies-arrayexpress

Splicing_Arrays_2

2008-12-30 | GSE13944 | GEO

Splicing_Arrays_1

2008-12-30 | GSE13943 | GEO

SL2_expression

2008-12-30 | GSE13942 | GEO

RIP_Chip_analysis

2008-12-30 | GSE13941 | GEO

High-resolution mapping defines the cooperative architecture of Polycomb Response Elements

Project description:Polycomb-mediated chromatin repression modulates gene expression during development in metazoans. Binding of multiple sequence-specific factors at discrete Polycomb Response Elements (PREs) is thought to recruit repressive complexes that spread across an extended chromatin domain. To dissect the structure of PREs, we applied high-resolution mapping of non-histone chromatin proteins in native chromatin of Drosophila cells. Analysis of occupied sites reveal cooperative interactions between transcription factors that stabilize Polycomb anchoring to DNA, and implicate the general transcription factor Adf1 as a novel PRE component. By comparing two Drosophila cell lines with differential chromatin states, we provide evidence that repression is accomplished at multiple steps in transcription, including inactivation of distant enhancers, enhanced Polycomb recruitment to PREs and target promoters, and elevated stalling of RNAPII in repressed genes. These results suggest that the stability of complexes bridging promoters, enhancers, and PREs is a crucial aspect of developmentally regulated gene expression. Native chromatin immunoprecipitation of histones, transcription factors and Polycomb protein in Drosophila cell lines.

2014-02-08 | E-GEOD-47829 | biostudies-arrayexpress

Budding yeast RNA polymerase II CTD phosphorylation and transcription termination factor localization

Project description:Whole genome analysis of total RNA pol II, Ser2-, Ser5- and Ser7-phosphorylated RNA pol II, in WT and mutants of the C-terminal domain (CTD) kinases Ctk1 and Kin28, and localization of the termination factors Pcf11, Nrd1 and Rat1. ChIP-chip using ligation-mediated PCR-amplified material hybridized to NimbleGen 385K arrays (50mers, median probe spacing 32 bp, cat. No. C4214-00-01).

2010-09-15 | E-GEOD-23960 | biostudies-arrayexpress

MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma (RNA-Seq)

Project description:We knock down MYCN in human neuroblastoma cell line by RNAi. MYCN knock-down caused global epigenome change, including nucleosome gain on key DNA-repair genes and promoter H3K9ac down regulation.

2019-06-30 | GSE120858 | GEO

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