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Identification of protein-RNA interactions in Drosophila using RIP-Seq

experiment: Identification of protein-RNA interactions in Drosophila using RIP-Seq project: The Drosophila Transcriptome PI: Sue Celniker Labs: Brenton Graveley
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 using Illumina Tru-Seq mRNA kits and sequenced on the Illumina GAIIx or HiSeq2000. Sequence reads were aligned to the D. melanogaster reference genome r5 using TopHat and expression levels were quantitated using Cufflinks.
There are 30 RIP-seq submissions for this experiment:
DCC id Name cell line Embargoed until Features, GBrowse and Data Files
modENCODE_5427


Related to: modENCODE_5468

RIP-Seq of D. melanogster splicing factors CG8636 sequences S2R+-CG8636 [ALL]
embargo expired SRA: SRR494071
SRA: SRR494072


2 files Download data files
modENCODE_5407


Related to: modENCODE_5448

RIP-Seq of D. melanogster splicing factors CG16901 sequences S2R+-CG16901 [ALL]
embargo expired SRA: SRR494034
SRA: SRR494035


2 files Download data files
modENCODE_5426


Related to: modENCODE_5467

RIP-Seq of D. melanogster splicing factors CG7437 sequences S2R+-CG7437 [ALL]
embargo expired SRA: SRR494069
SRA: SRR494070


2 files Download data files
modENCODE_5408


Related to: modENCODE_5449

RIP-Seq of D. melanogster splicing factors CG17136 sequences S2R+-CG17136 [ALL]
embargo expired SRA: SRR494036
SRA: SRR494037


2 files Download data files
modENCODE_5429


Related to: modENCODE_5470

RIP-Seq of D. melanogster splicing factors CG9998 sequences S2R+-CG9998 [ALL]
embargo expired SRA: SRR494075
SRA: SRR494076


2 files Download data files
modENCODE_5409


Related to: modENCODE_5450

RIP-Seq of D. melanogster splicing factors CG17838 sequences S2R+-CG17838 [ALL]
embargo expired SRA: SRR494038
SRA: SRR494039


2 files Download data files
modENCODE_5428


Related to: modENCODE_5469

RIP-Seq of D. melanogster splicing factors CG8749 sequences S2R+-CG8749 [ALL]
embargo expired SRA: SRR494073
SRA: SRR494074


2 files Download data files
modENCODE_5410


Related to: modENCODE_5451

RIP-Seq of D. melanogster splicing factors CG31716 sequences S2R+-CG31716 [ALL]
embargo expired SRA: SRR494040
SRA: SRR494041


2 files Download data files
modENCODE_5412


Related to: modENCODE_5453

RIP-Seq of D. melanogster splicing factors CG3613 sequences S2R+-CG3613 [ALL]
embargo expired SRA: SRR494042
SRA: SRR494043


2 files Download data files
modENCODE_5430


Related to: modENCODE_5471

RIP-Seq of D. melanogster splicing factors Empty Vector sequences S2R+-pMK33-C-FLAG-HA Empty Vector [ALL]
embargo expired SRA: SRR494077
SRA: SRR494078
SRA: SRR494079
SRA: SRR494081
SRA: SRR494083


5 files Download data files
modENCODE_5413


Related to: modENCODE_5454

RIP-Seq of D. melanogster splicing factors CG4262 sequences S2R+-CG4262 [ALL]
embargo expired SRA: SRR494044
SRA: SRR494045


2 files Download data files
modENCODE_5414


Related to: modENCODE_5455

RIP-Seq of D. melanogster splicing factors CG42670 sequences S2R+-CG42670 [ALL]
embargo expired SRA: SRR494046
SRA: SRR494047
SRA: SRR494048


3 files Download data files
modENCODE_5415


Related to: modENCODE_5456

RIP-Seq of D. melanogster splicing factors CG4602 sequences S2R+-CG4602 [ALL]
embargo expired SRA: SRR494049
SRA: SRR494050


2 files Download data files
modENCODE_5398


Related to: modENCODE_5439

RIP-Seq of D. melanogster splicing factors CG10203 sequences S2R+-CG10203 [ALL]
embargo expired SRA: SRR494016
SRA: SRR494017


2 files Download data files
modENCODE_5417


Related to: modENCODE_5458

RIP-Seq of D. melanogster splicing factors CG5099 sequences S2R+-CG5099 [ALL]
embargo expired SRA: SRR494053
SRA: SRR494054


2 files Download data files
modENCODE_5399


Related to: modENCODE_5440

RIP-Seq of D. melanogster splicing factors CG10279 sequences S2R+-CG10279 [ALL]
embargo expired SRA: SRR494018
SRA: SRR494019


2 files Download data files
modENCODE_5416


Related to: modENCODE_5457

RIP-Seq of D. melanogster splicing factors CG4816 sequences S2R+-CG4816 [ALL]
embargo expired SRA: SRR494051
SRA: SRR494052


2 files Download data files
modENCODE_5400


Related to: modENCODE_5441

RIP-Seq of D. melanogster splicing factors CG10851 sequences S2R+-CG10851 [ALL]
embargo expired SRA: SRR494020
SRA: SRR494021


2 files Download data files
modENCODE_5421


Related to: modENCODE_5462

RIP-Seq of D. melanogster splicing factors CG6203 sequences S2R+-CG6203 [ALL]
embargo expired SRA: SRR494057
SRA: SRR494058
SRA: SRR494059


3 files Download data files
modENCODE_5401


Related to: modENCODE_5442

RIP-Seq of D. melanogster splicing factors CG12357 sequences S2R+-CG12357 [ALL]
embargo expired SRA: SRR494022
SRA: SRR494023


2 files Download data files
modENCODE_5418


Related to: modENCODE_5459

RIP-Seq of D. melanogster splicing factors CG5442 sequences S2R+-CG5442 [ALL]
embargo expired SRA: SRR494055
SRA: SRR494056


2 files Download data files
modENCODE_5402


Related to: modENCODE_5443

RIP-Seq of D. melanogster splicing factors CG12749 sequences S2R+-CG12749 [ALL]
embargo expired SRA: SRR494024
SRA: SRR494025


2 files Download data files
modENCODE_5423


Related to: modENCODE_5464

RIP-Seq of D. melanogster splicing factors CG6779 sequences S2R+-CG6779 [ALL]
embargo expired SRA: SRR494062
SRA: SRR494063
SRA: SRR494064


3 files Download data files
modENCODE_5403


Related to: modENCODE_5444

RIP-Seq of D. melanogster splicing factors CG1559 sequences S2R+-CG1559 [ALL]
embargo expired SRA: SRR494026
SRA: SRR494027


2 files Download data files
modENCODE_5422


Related to: modENCODE_5463

RIP-Seq of D. melanogster splicing factors CG6227 sequences S2R+-CG6227 [ALL]
embargo expired SRA: SRR494060
SRA: SRR494061


2 files Download data files
modENCODE_5405


Related to: modENCODE_5446

RIP-Seq of D. melanogster splicing factors CG16725 sequences S2R+-CG16725 [ALL]
embargo expired SRA: SRR494028
SRA: SRR494029
SRA: SRR494030


3 files Download data files
modENCODE_5397


Related to: modENCODE_5438

RIP-Seq of D. melanogster splicing factors CG10128 sequences S2R+-CG10128 [ALL]
embargo expired SRA: SRR494014
SRA: SRR494015


2 files Download data files
modENCODE_5425


Related to: modENCODE_5466

RIP-Seq of D. melanogster splicing factors CG6987 sequences S2R+-CG6987 [ALL]
embargo expired SRA: SRR494067
SRA: SRR494068


2 files Download data files
modENCODE_5406


Related to: modENCODE_5447

RIP-Seq of D. melanogster splicing factors CG16788 sequences S2R+-CG16788 [ALL]
embargo expired SRA: SRR494031
SRA: SRR494032
SRA: SRR494033


3 files Download data files
modENCODE_5424


Related to: modENCODE_5465

RIP-Seq of D. melanogster splicing factors CG6841 sequences S2R+-CG6841 [ALL]
embargo expired SRA: SRR494065
SRA: SRR494066


2 files Download data files