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Title: Identification of protein-RNA interactions in Drosophila using RIP-Seq      
dateReleased:
05-05-2012
description:
The goal of these experiments is to identify RNAs bound by individual RNA-binding proteins. Drosophila S2R+ cells were transiently transfected with vectors encoding the indicated HA-tagged RNA-binding proteins, or without an insert as a control. Expression was induced with CuSO4, whole cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation with HA immunoaffinity resin. RNA was then isolated from the immunoprecipitated material, and RNA-Seq libraries were prepared and sequenced. Sequence reads were aligned to the D. melanogaster reference genome Dm3 using TopHat and expression levels were quantitated using cufflinks. This work was funded as part of the modENCODE project by NHGRI. For data usage terms and conditions, please refer to and At least two biological replicates were performed for each protein studied. In addition, control experiments were performed in which cells were transfected with the same vector lacking an open reading frame.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-37756
refinement:
raw
alternateIdentifiers:
37756
keywords:
functional genomics
dateModified:
05-03-2014
availability:
available
types:
gene expression
name:
Drosophila melanogaster
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-37756/E-GEOD-37756.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-37756/E-GEOD-37756.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37756
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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