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Tissue-specific Transcriptional Profiling of D. melanogaster using Illumina poly(A)+ RNA-Seq

experiment: Tissue-specific Transcriptional Profiling of D. melanogaster using Illumina poly(A)+ RNA-Seq project: The Drosophila Transcriptome PI: Sue Celniker Labs: Brenton Graveley
RNA-seq analysis was performed on poly(A)+ RNA from various tissues dissected from various stages of D. melanogaster. Total RNA was isolated by the Peter Cherbas group. Isolation of poly(A)+ RNA and strand-specific library construction were performed in the Brenton Graveley lab. Libraries were distributed among 3 labs in the Drosophila Transcriptome group for sequencing (Celniker, Gingeras, and Graveley) for paired-end RNA sequencing (2x76+ nt) on the GAIIx platform. Fastq files were generated using pipeline version 1.5. Reads were aligned to the genome and a splice-junction database using Bowtie 0.12.0-beta1 and SPA5.pl (to identify only uniquely-mapped reads).
There are 31 RNA-seq submissions for this experiment:
DCC id Name developmental stage strain tissue Embargoed until Features, GBrowse and Data Files
modENCODE_4268


Related to: modENCODE_3207
modENCODE_4318
modENCODE_4669

Dm Tissue Expression RNA-seq WPP fat body sequences pupae [ALL]
L3 stage wandering larvae [ALL]
White prepupae (WPP) [ALL]
Oregon-R-modENCODE [ALL]
fat body [ALL]
embargo expired SRA: SRR070411
SRA: SRR070428
Download data files
modENCODE_4267


Related to: modENCODE_3207
modENCODE_4317
modENCODE_4668

Dm Tissue Expression RNA-seq WPP+2d fat sequences pupae [ALL]
L3 stage wandering larvae [ALL]
White prepupae (WPP) [ALL]
Oregon-R-modENCODE [ALL]
fat body [ALL]
embargo expired SRA: SRR070413
SRA: SRR070429
Download data files
modENCODE_4266


Related to: modENCODE_3207
modENCODE_4316
modENCODE_4667

Dm Tissue Expression RNA-seq virgin female eclosion + 4 days ovaries sequences virgin female [ALL]
Oregon-R-modENCODE [ALL]
virgin adult ovaries [ALL]
embargo expired SRA: SRR070396
SRA: SRR070417
Download data files
modENCODE_4265


Related to: modENCODE_3207
modENCODE_4315
modENCODE_4666

Dm Tissue Expression RNA-seq virgin female eclosion + 4 days heads sequences virgin female [ALL]
adult virgin female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070430
SRA: SRR100278
SRA: SRR100282
Download data files
modENCODE_4264


Related to: modENCODE_3207
modENCODE_4314
modENCODE_4665

Dm Tissue Expression RNA-seq virgin female eclosion + 20 days heads sequences virgin female [ALL]
adult virgin female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070388
SRA: SRR070419
SRA: SRR100275
Download data files
modENCODE_4263


Related to: modENCODE_3207
modENCODE_4313
modENCODE_4664

Dm Tissue Expression RNA-seq virgin female eclosion + 1 day heads sequences virgin female [ALL]
adult virgin female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070436
SRA: SRR070437
SRA: SRR100281
Download data files
modENCODE_4262


Related to: modENCODE_3207
modENCODE_4312
modENCODE_4663

Dm Tissue Expression RNA-seq third instar larvae wandering stage salivary glands sequences L3 stage wandering larvae [ALL]
White prepupae (WPP) [ALL]
Oregon-R-modENCODE [ALL]
salivary glands [ALL]
embargo expired SRA: SRR070407
SRA: SRR070425
Download data files
modENCODE_3445


Related to: modENCODE_3207

Tissues mixed males and females, eclosion + 1 day, digestive system RNA-Seq uniquely mapped reads L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired SRA: SRR070394
SRA: SRR070398


2 files Download data files
modENCODE_3446


Related to: modENCODE_3207

Tissues mixed males and females, eclosion + 1 day, carcass RNA-Seq uniquely mapped reads L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
carcass [ALL]
embargo expired SRA: SRR070395
SRA: SRR070399


2 files Download data files
modENCODE_4242


Related to: modENCODE_3207
modENCODE_4292
modENCODE_4643

Dm Tissue Expression RNA-seq mated female eclosion + 20 days heads sequences adult mated female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070420
SRA: SRR100274
SRA: SRR111882
SRA: SRR116383
Download data files
modENCODE_4245


Related to: modENCODE_3207
modENCODE_4295
modENCODE_4646

Dm Tissue Expression RNA-seq mated male eclosion + 1 day heads sequences adult male [ALL]
Adult male eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070432
SRA: SRR070433
SRA: SRR100280
Download data files
modENCODE_4241


Related to: modENCODE_3207
modENCODE_4291
modENCODE_4642

Dm Tissue Expression RNA-seq mated female eclosion + 1 day heads sequences adult mated female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070434
SRA: SRR070435
SRA: SRR100279
Download data files
modENCODE_4243


Related to: modENCODE_3207
modENCODE_4293
modENCODE_4644

Dm Tissue Expression RNA-seq mated female eclosion + 4 days heads sequences adult mated female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070414
SRA: SRR070415
Download data files
modENCODE_4244


Related to: modENCODE_3207
modENCODE_4294
modENCODE_4645

Dm Tissue Expression RNA-seq mated female eclosion + 4 days ovaries sequences adult mated female [ALL]
Oregon-R-modENCODE [ALL]
mated adult ovaries [ALL]
embargo expired SRA: SRR070431
SRA: SRR100277
SRA: SRR100283
Download data files
modENCODE_4252


Related to: modENCODE_3207
modENCODE_4302
modENCODE_4653

Dm Tissue Expression RNA-seq mixed males and females eclosion + 20 days carcass sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
carcass [ALL]
embargo expired SRA: SRR070391
SRA: SRR070404
Download data files
modENCODE_4253


Related to: modENCODE_3207
modENCODE_4303
modENCODE_4654

Dm Tissue Expression RNA-seq mixed males and females eclosion + 20 days digestive system sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired SRA: SRR070390
SRA: SRR070403
SRA: SRR111883
Download data files
modENCODE_4250


Related to: modENCODE_3207
modENCODE_4300
modENCODE_4651

Dm Tissue Expression RNA-seq mixed males and females eclosion + 1 day carcass sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
carcass [ALL]
embargo expired SRA: SRR070395
SRA: SRR070399
Download data files
modENCODE_4251


Related to: modENCODE_3207
modENCODE_4301
modENCODE_4652

Dm Tissue Expression RNA-seq mixed males and females eclosion + 1 day digestive system sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired SRA: SRR070394
SRA: SRR070398
Download data files
modENCODE_4249


Related to: modENCODE_3207
modENCODE_4299
modENCODE_4650

Dm Tissue Expression RNA-seq mated male eclosion + 4 days testes sequences adult male [ALL]
Oregon-R-modENCODE [ALL]
testes [ALL]
embargo expired SRA: SRR070422
SRA: SRR070423
SRA: SRR100276
SRA: SRR350960
SRA: SRR350961
Download data files
modENCODE_4248


Related to: modENCODE_3207
modENCODE_4298
modENCODE_4649

Dm Tissue Expression RNA-seq mated male eclosion + 4 days heads sequences adult male [ALL]
Adult male eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070400
SRA: SRR070416
Download data files
modENCODE_4247


Related to: modENCODE_3207
modENCODE_4297
modENCODE_4648

Dm Tissue Expression RNA-seq mated male eclosion + 4 days accessory glands sequences adult male [ALL]
Oregon-R-modENCODE [ALL]
male accessory glands [ALL]
embargo expired SRA: SRR070397
SRA: SRR070418
SRA: SRR100272
SRA: SRR100273
SRA: SRR111880
...All entries in public repositories generated by this submission

Download data files
modENCODE_4246


Related to: modENCODE_3207
modENCODE_4296
modENCODE_4647

Dm Tissue Expression RNA-seq mated male eclosion + 20 days heads sequences adult male [ALL]
Adult male eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired SRA: SRR070421
SRA: SRR070424
Download data files
modENCODE_4259


Related to: modENCODE_3207
modENCODE_4309
modENCODE_4660

Dm Tissue Expression RNA-seq third instar larvae wandering stage digestive system sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired SRA: SRR070408
SRA: SRR100268
Download data files
modENCODE_4260


Related to: modENCODE_3207
modENCODE_4310
modENCODE_4661

Dm Tissue Expression RNA-seq third instar larvae wandering stage fat body sequences pupae [ALL]
L3 stage wandering larvae [ALL]
White prepupae (WPP) [ALL]
Oregon-R-modENCODE [ALL]
fat body [ALL]
embargo expired SRA: SRR070405
SRA: SRR070406
Download data files
modENCODE_4261


Related to: modENCODE_3207
modENCODE_4311
modENCODE_4662

Dm Tissue Expression RNA-seq third instar larvae wandering stage imaginal discs sequences L3 stage wandering larvae [ALL]
Oregon-R-modENCODE [ALL]
imaginal discs [ALL]
embargo expired SRA: SRR070392
SRA: SRR070393
SRA: SRR111884
SRA: SRR111885
SRA: SRR350962
...All entries in public repositories generated by this submission

Download data files
modENCODE_4256


Related to: modENCODE_3207
modENCODE_4306
modENCODE_4657

Dm Tissue Expression RNA-seq Pupae WPP+2d CNS sequences Pupae [ALL]
L3 stage wandering larvae [ALL]
Oregon-R-modENCODE [ALL]
central nervous system [ALL]
embargo expired SRA: SRR070412
SRA: SRR100271
Download data files
modENCODE_4257


Related to: modENCODE_3207
modENCODE_4307
modENCODE_4658

Dm Tissue Expression RNA-seq third instar larvae CNS sequences Pupae [ALL]
L3 stage wandering larvae [ALL]
Oregon-R-modENCODE [ALL]
central nervous system [ALL]
embargo expired SRA: SRR070409
SRA: SRR070410
Download data files
modENCODE_4258


Related to: modENCODE_3207
modENCODE_4308
modENCODE_4659

Dm Tissue Expression RNA-seq third instar larvae wandering stage carcass sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
carcass [ALL]
embargo expired SRA: SRR070426
SRA: SRR100269
Download data files
modENCODE_4269


Related to: modENCODE_3207
modENCODE_4319
modENCODE_4670

Dm Tissue Expression RNA-seq WPP salivary glands sequences L3 stage wandering larvae [ALL]
White prepupae (WPP) [ALL]
Oregon-R-modENCODE [ALL]
salivary glands [ALL]
embargo expired SRA: SRR070427
SRA: SRR100270
Download data files
modENCODE_4254


Related to: modENCODE_3207
modENCODE_4304
modENCODE_4655

Dm Tissue Expression RNA-seq mixed males and females eclosion + 4 days carcass sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
carcass [ALL]
embargo expired SRA: SRR070387
SRA: SRR070402
Download data files
modENCODE_4255


Related to: modENCODE_3207
modENCODE_4305
modENCODE_4656

Dm Tissue Expression RNA-seq mixed males and females eclosion + 4 days digestive system sequences L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired SRA: SRR070386
SRA: SRR070401
SRA: SRR111878
SRA: SRR111879
Download data files