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

experiment: Identification of protein-RNA interactions in Drosophila using RIP-Seq TopHat analysis 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.

NO FEATURES GENERATED BY THIS EXPERIMENT All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All entries in public repositories generated by this experiment
There are 30 Computational annotation submissions for this experiment:
DCC id Name cell line Embargoed until Features, GBrowse and Data Files
modENCODE_5467


Related to: modENCODE_5426

RIP-Seq of D. melanogster splicing factors CG7437 r5 alignments S2R+-CG7437 [ALL]
embargo expired
GBrowse tracks: submission_5467.sorted
GEO: GSM927220
GEO: GSM927221


4 files Download data files
modENCODE_5447


Related to: modENCODE_5406

RIP-Seq of D. melanogster splicing factors CG16788 r5 alignments S2R+-CG16788 [ALL]
embargo expired
GBrowse tracks: submission_5447.sorted
GEO: GSM927182
GEO: GSM927183
GEO: GSM927184


6 files Download data files
modENCODE_5448


Related to: modENCODE_5407

RIP-Seq of D. melanogster splicing factors CG16901 r5 alignments S2R+-CG16901 [ALL]
embargo expired
GBrowse tracks: submission_5448.sorted
GEO: GSM927185
GEO: GSM927186


4 files Download data files
modENCODE_5466


Related to: modENCODE_5425

RIP-Seq of D. melanogster splicing factors CG6987 r5 alignments S2R+-CG6987 [ALL]
embargo expired
GBrowse tracks: submission_5466.sorted
GEO: GSM927218
GEO: GSM927219


4 files Download data files
modENCODE_5469


Related to: modENCODE_5428

RIP-Seq of D. melanogster splicing factors CG8749 r5 alignments S2R+-CG8749 [ALL]
embargo expired
GBrowse tracks: submission_5469.sorted
GEO: GSM927224
GEO: GSM927225


4 files Download data files
modENCODE_5449


Related to: modENCODE_5408

RIP-Seq of D. melanogster splicing factors CG17136 r5 alignments S2R+-CG17136 [ALL]
embargo expired
GBrowse tracks: submission_5449.sorted
GEO: GSM927187
GEO: GSM927188


4 files Download data files
modENCODE_5468


Related to: modENCODE_5427

RIP-Seq of D. melanogster splicing factors CG8636 r5 alignments S2R+-CG8636 [ALL]
embargo expired
GBrowse tracks: submission_5468.sorted
GEO: GSM927222
GEO: GSM927223


4 files Download data files
modENCODE_5450


Related to: modENCODE_5409

RIP-Seq of D. melanogster splicing factors CG17838 r5 alignments S2R+-CG17838 [ALL]
embargo expired
GBrowse tracks: submission_5450.sorted
GEO: GSM927189
GEO: GSM927190


4 files Download data files
modENCODE_5471


Related to: modENCODE_5430

RIP-Seq of D. melanogster splicing factors Empty Vector r5 alignments S2R+-pMK33-C-FLAG-HA Empty Vector [ALL]
embargo expired
GBrowse tracks: submission_5471.sorted
GEO: GSM927228
GEO: GSM927229
GEO: GSM927230
GEO: GSM927232
GEO: GSM927234


10 files Download data files
modENCODE_5451


Related to: modENCODE_5410

RIP-Seq of D. melanogster splicing factors CG31716 r5 alignments S2R+-CG31716 [ALL]
embargo expired
GBrowse tracks: submission_5451.sorted
GEO: GSM927191
GEO: GSM927192


4 files Download data files
modENCODE_5470


Related to: modENCODE_5429

RIP-Seq of D. melanogster splicing factors CG9998 r5 alignments S2R+-CG9998 [ALL]
embargo expired
GBrowse tracks: submission_5470.sorted
GEO: GSM927226
GEO: GSM927227


4 files Download data files
modENCODE_5453


Related to: modENCODE_5412

RIP-Seq of D. melanogster splicing factors CG3613 r5 alignments S2R+-CG3613 [ALL]
embargo expired
GBrowse tracks: submission_5453.sorted
GEO: GSM927193
GEO: GSM927194


4 files Download data files
modENCODE_5454


Related to: modENCODE_5413

RIP-Seq of D. melanogster splicing factors CG4262 r5 alignments S2R+-CG4262 [ALL]
embargo expired
GBrowse tracks: submission_5454.sorted
GEO: GSM927195
GEO: GSM927196


4 files Download data files
modENCODE_5455


Related to: modENCODE_5414

RIP-Seq of D. melanogster splicing factors CG42670 r5 alignments S2R+-CG42670 [ALL]
embargo expired
GBrowse tracks: submission_5455.sorted
GEO: GSM927197
GEO: GSM927198
GEO: GSM927199


6 files Download data files
modENCODE_5438


Related to: modENCODE_5397

RIP-Seq of D. melanogster splicing factors CG10128 r5 alignments S2R+-CG10128 [ALL]
embargo expired
GBrowse tracks: submission_5438.sorted
GEO: GSM927165
GEO: GSM927166


4 files Download data files
modENCODE_5457


Related to: modENCODE_5416

RIP-Seq of D. melanogster splicing factors CG4816 r5 alignments S2R+-CG4816 [ALL]
embargo expired
GBrowse tracks: submission_5457.sorted
GEO: GSM927202
GEO: GSM927203


4 files Download data files
modENCODE_5439


Related to: modENCODE_5398

RIP-Seq of D. melanogster splicing factors CG10203 r5 alignments S2R+-CG10203 [ALL]
embargo expired
GBrowse tracks: submission_5439.sorted
GEO: GSM927167
GEO: GSM927168


4 files Download data files
modENCODE_5456


Related to: modENCODE_5415

RIP-Seq of D. melanogster splicing factors CG4602 r5 alignments S2R+-CG4602 [ALL]
embargo expired
GBrowse tracks: submission_5456.sorted
GEO: GSM927200
GEO: GSM927201


4 files Download data files
modENCODE_5440


Related to: modENCODE_5399

RIP-Seq of D. melanogster splicing factors CG10279 r5 alignments S2R+-CG10279 [ALL]
embargo expired
GBrowse tracks: submission_5440.sorted
GEO: GSM927169
GEO: GSM927170


4 files Download data files
modENCODE_5459


Related to: modENCODE_5418

RIP-Seq of D. melanogster splicing factors CG5442 r5 alignments S2R+-CG5442 [ALL]
embargo expired
GBrowse tracks: submission_5459.sorted
GEO: GSM927206
GEO: GSM927207


4 files Download data files
modENCODE_5441


Related to: modENCODE_5400

RIP-Seq of D. melanogster splicing factors CG10851 r5 alignments S2R+-CG10851 [ALL]
embargo expired
GBrowse tracks: submission_5441.sorted
GEO: GSM927171
GEO: GSM927172


4 files Download data files
modENCODE_5458


Related to: modENCODE_5417

RIP-Seq of D. melanogster splicing factors CG5099 r5 alignments S2R+-CG5099 [ALL]
embargo expired
GBrowse tracks: submission_5458.sorted
GEO: GSM927204
GEO: GSM927205


4 files Download data files
modENCODE_5442


Related to: modENCODE_5401

RIP-Seq of D. melanogster splicing factors CG12357 r5 alignments S2R+-CG12357 [ALL]
embargo expired
GBrowse tracks: submission_5442.sorted
GEO: GSM927173
GEO: GSM927174


4 files Download data files
modENCODE_5463


Related to: modENCODE_5422

RIP-Seq of D. melanogster splicing factors CG6227 r5 alignments S2R+-CG6227 [ALL]
embargo expired
GBrowse tracks: submission_5463.sorted
GEO: GSM927211
GEO: GSM927212


4 files Download data files
modENCODE_5443


Related to: modENCODE_5402

RIP-Seq of D. melanogster splicing factors CG12749 r5 alignments S2R+-CG12749 [ALL]
embargo expired
GBrowse tracks: submission_5443.sorted
GEO: GSM927175
GEO: GSM927176


4 files Download data files
modENCODE_5462


Related to: modENCODE_5421

RIP-Seq of D. melanogster splicing factors CG6203 r5 alignments S2R+-CG6203 [ALL]
embargo expired
GBrowse tracks: submission_5462.sorted
GEO: GSM927208
GEO: GSM927209
GEO: GSM927210


6 files Download data files
modENCODE_5444


Related to: modENCODE_5403

RIP-Seq of D. melanogster splicing factors CG1559 r5 alignments S2R+-CG1559 [ALL]
embargo expired
GBrowse tracks: submission_5444.sorted
GEO: GSM927177
GEO: GSM927178


4 files Download data files
modENCODE_5465


Related to: modENCODE_5424

RIP-Seq of D. melanogster splicing factors CG6841 r5 alignments S2R+-CG6841 [ALL]
embargo expired
GBrowse tracks: submission_5465.sorted
GEO: GSM927216
GEO: GSM927217


4 files Download data files
modENCODE_5446


Related to: modENCODE_5405

RIP-Seq of D. melanogster splicing factors CG16725 r5 alignments S2R+-CG16725 [ALL]
embargo expired
GBrowse tracks: submission_5446.sorted
GEO: GSM927179
GEO: GSM927180
GEO: GSM927181


6 files Download data files
modENCODE_5464


Related to: modENCODE_5423

RIP-Seq of D. melanogster splicing factors CG6779 r5 alignments S2R+-CG6779 [ALL]
embargo expired
GBrowse tracks: submission_5464.sorted
GEO: GSM927213
GEO: GSM927214
GEO: GSM927215


6 files Download data files