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Cap Analysis of Gene Expression

experiment: Cap Analysis of Gene Expression project: The Drosophila Transcriptome PI: Sue Celniker Labs: Sue Celniker
To map transcription start sites (TSSs) genome-wide, we perform CAGE (Cap Analysis of Gene Expression). These CAGE tags are 27-nt sequences that are derived from mRNAs and other long capped transcripts in the vicinity of the 5' cap site. Their mapping onto the genome sequence defines TSSs. CAGE libraries are constructed from first-strand cDNA selected through a biotinylated cap. Second-strand synthesis is dependent upon ligation to the first-strand full-length cDNA of a primer that contains a restriction site for a type II endonuclease allowing the cleavage of 5' 27-bp tags from the resulting cDNA. These short fragments are sequenced using the Illumina GA platform.

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 43 CAGE submissions for this experiment:
DCC id Name developmental stage cell line strain tissue Embargoed until Features, GBrowse and Data Files
modENCODE_5371

CAGE Dpse Ovaries Reproductive Tract embargo expired SRA: SRR488319


3 files Download data files
modENCODE_5332


Related to: modENCODE_3971

CAGE kc167 Cytoplasm RNA (2 reps) Kc167 [ALL]
embargo expired
GBrowse tracks: submission_5332.sorted
SRA: SRR488273
SRA: SRR488275


4 files Download data files
modENCODE_5353


Related to: modENCODE_3207

CAGE MixMF 4d carcass L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
carcass [ALL]
embargo expired
GBrowse tracks: submission_5353.sorted
SRA: SRR488325


3 files Download data files
modENCODE_5352


Related to: modENCODE_3207

CAGE L3 Wand carcass L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
carcass [ALL]
embargo expired
GBrowse tracks: submission_5352.sorted
SRA: SRR488324


3 files Download data files
modENCODE_5333


Related to: modENCODE_3970

CAGE kc167 Nuclear RNA (2 reps) Kc167 [ALL]
embargo expired
GBrowse tracks: submission_5333.sorted
SRA: SRR488274
SRA: SRR488276


4 files Download data files
modENCODE_5369

CAGE Dpse F Carcass Rep Tract embargo expired SRA: SRR488317


3 files Download data files
modENCODE_5370

CAGE Dpse M Carcass Rep Tract embargo expired SRA: SRR488318


3 files Download data files
modENCODE_5366


Related to: modENCODE_3207

CAGE AdMateM 4d testes (2 reps) adult male [ALL]
Oregon-R-modENCODE [ALL]
testes [ALL]
embargo expired
GBrowse tracks: submission_5366.sorted
SRA: SRR488284
SRA: SRR488285
SRA: SRR488308
SRA: SRR488309


4 files Download data files
modENCODE_2549


Related to: modENCODE_574

CAGE sequencing of mixed embryo 5' ends Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: Celniker_CAGE_Illumina
Dm_CAGE_HYB
SRA: SRX015329


3 files Download data files
modENCODE_5367


Related to: modENCODE_3207

CAGE AdMateF 4d ovaries adult mated female [ALL]
Oregon-R-modENCODE [ALL]
mated adult ovaries [ALL]
embargo expired
GBrowse tracks: submission_5367.sorted
SRA: SRR488282


3 files Download data files
modENCODE_5368


Related to: modENCODE_3207

CAGE AdVirF 4d ovaries virgin female [ALL]
Oregon-R-modENCODE [ALL]
virgin adult ovaries [ALL]
embargo expired
GBrowse tracks: submission_5368.sorted
SRA: SRR488283


3 files Download data files
modENCODE_5335


Related to: modENCODE_5519

CAGE BG3-c2 whole cell 0hr ecdysone ML-DmBG3-c2 [ALL]
embargo expired
GBrowse tracks: submission_5335.sorted
SRA: SRR488314


3 files Download data files
modENCODE_5336


Related to: modENCODE_5519

CAGE BG3-c2 whole cell 5hr ecdysone ML-DmBG3-c2 [ALL]
embargo expired
GBrowse tracks: submission_5336.sorted
SRA: SRR488315


3 files Download data files
modENCODE_5337


Related to: modENCODE_5519

CAGE BG3-c2 whole cell 24hr ecdysone ML-DmBG3-c2 [ALL]
embargo expired
GBrowse tracks: submission_5337.sorted
SRA: SRR488316


3 files Download data files
modENCODE_5338


Related to: modENCODE_574

CAGE em0-2hr Embryo 0-2 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5338.sorted
SRA: SRR488290
SRA: SRR488297


3 files Download data files
modENCODE_5339


Related to: modENCODE_574

CAGE em2-4hr Embryo 2-4 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5339.sorted
SRA: SRR488291
SRA: SRR488298


3 files Download data files
modENCODE_5340


Related to: modENCODE_574

CAGE em4-6hr Embryo 4-6 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5340.sorted
SRA: SRR488292


3 files Download data files
modENCODE_5341


Related to: modENCODE_574

CAGE em6-8hr Embryo 6-8 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5341.sorted
SRA: SRR488300


3 files Download data files
modENCODE_5343


Related to: modENCODE_574

CAGE em12-14hr Embryo 12-14 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5343.sorted
SRA: SRR488302


3 files Download data files
modENCODE_5342


Related to: modENCODE_574

CAGE em8-10hr Embryo 8-10 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5342.sorted
SRA: SRR488301


3 files Download data files
modENCODE_5357


Related to: modENCODE_3207

CAGE WPP 2d fat pupae [ALL]
L3 stage wandering larvae [ALL]
White prepupae (WPP) [ALL]
Oregon-R-modENCODE [ALL]
fat body [ALL]
embargo expired
GBrowse tracks: submission_5357.sorted
SRA: SRR488327


3 files Download data files
modENCODE_5345


Related to: modENCODE_574

CAGE em20-22hr Embryo 20-22 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5345.sorted
SRA: SRR488304


3 files Download data files
modENCODE_5344


Related to: modENCODE_574

CAGE em16-18hr Embryo 16-18 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5344.sorted
SRA: SRR488303


3 files Download data files
modENCODE_5356


Related to: modENCODE_3207

CAGE MixMF 20d dig sys L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired
GBrowse tracks: submission_5356.sorted
SRA: SRR488289


3 files Download data files
modENCODE_5347


Related to: modENCODE_574

CAGE L2 L2 stage larvae [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5347.sorted
SRA: SRR488293


3 files Download data files
modENCODE_5346


Related to: modENCODE_574

CAGE L1 L1 stage larvae [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5346.sorted
SRA: SRR488305


3 files Download data files
modENCODE_5355


Related to: modENCODE_3207

CAGE MixMF 4d dig sys L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired
GBrowse tracks: submission_5355.sorted
SRA: SRR488288


3 files Download data files
modENCODE_5349


Related to: modENCODE_574

CAGE L3 PS3-6 L3 stage larvae [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5349.sorted
SRA: SRR488294


3 files Download data files
modENCODE_5361


Related to: modENCODE_3207

CAGE AdMatedM Ecl 1day Heads Trizol Tissues adult male [ALL]
Adult male eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired
GBrowse tracks: submission_5361.sorted
SRA: SRR488272
SRA: SRR488278


3 files Download data files
modENCODE_5348


Related to: modENCODE_574

CAGE L3 12hr L3 stage larvae [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5348.sorted
SRA: SRR488306


3 files Download data files
modENCODE_5354


Related to: modENCODE_3207

CAGE L3 Wand dig sys L3 stage wandering larvae [ALL]
adult [ALL]
Oregon-R-modENCODE [ALL]
digestive system [ALL]
embargo expired
GBrowse tracks: submission_5354.sorted
SRA: SRR488326


3 files Download data files
modENCODE_5331


Related to: modENCODE_3972

CAGE S2-DRSC whole cell (2 reps) S2-DRSC [ALL]
embargo expired
GBrowse tracks: submission_5331.sorted
SRA: SRR488286
SRA: SRR488287


4 files Download data files
modENCODE_5351


Related to: modENCODE_574

CAGE WPP 2days Pupae [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5351.sorted
SRA: SRR488296


3 files Download data files
modENCODE_5350


Related to: modENCODE_574

CAGE WPP 12hr White prepupae (WPP) + 12 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
GBrowse tracks: submission_5350.sorted
SRA: SRR488295


3 files Download data files
modENCODE_5360


Related to: modENCODE_3207

CAGE AdMatedF Ecl 1day Heads Trizol Tissues adult mated female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired
GBrowse tracks: submission_5360.sorted
SRA: SRR488271
SRA: SRR488277


3 files Download data files
modENCODE_5358


Related to: modENCODE_3207

CAGE L3 CNS Pupae [ALL]
L3 stage wandering larvae [ALL]
Oregon-R-modENCODE [ALL]
central nervous system [ALL]
embargo expired
GBrowse tracks: submission_5358.sorted
SRA: SRR488299
SRA: SRR488321


3 files Download data files
modENCODE_5359


Related to: modENCODE_3207

CAGE Pup WPP 2d CNS Pupae [ALL]
L3 stage wandering larvae [ALL]
Oregon-R-modENCODE [ALL]
central nervous system [ALL]
embargo expired
GBrowse tracks: submission_5359.sorted
SRA: SRR488322


3 files Download data files
modENCODE_5364


Related to: modENCODE_3207

CAGE L3 Wand imag disc L3 stage wandering larvae [ALL]
Oregon-R-modENCODE [ALL]
imaginal discs [ALL]
embargo expired
GBrowse tracks: submission_5364.sorted
SRA: SRR488281
SRA: SRR488310
SRA: SRR488311
SRA: SRR488312
SRA: SRR488313


3 files Download data files
modENCODE_5365


Related to: modENCODE_3207

CAGE AdMateM 4d acc gland adult male [ALL]
Oregon-R-modENCODE [ALL]
male accessory glands [ALL]
embargo expired
GBrowse tracks: submission_5365.sorted
SRA: SRR488323


3 files Download data files
modENCODE_5334


Related to: modENCODE_3972
modENCODE_5519

CAGE BG3-c2 whole cell (2 reps) ML-DmBG3-c2 [ALL]
embargo expired
GBrowse tracks: submission_5334.sorted
SRA: SRR488307
SRA: SRR488314


4 files Download data files
modENCODE_5372

CAGE Dpse Testes Reproductive Tract embargo expired SRA: SRR488320


3 files Download data files
modENCODE_5362


Related to: modENCODE_3207

CAGE AdMateF 20d head adult mated female [ALL]
Adult virgin female eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired
GBrowse tracks: submission_5362.sorted
SRA: SRR488279


3 files Download data files
modENCODE_5363


Related to: modENCODE_3207

CAGE AdMateM 20d head adult male [ALL]
Adult male eclosion+1 day [ALL]
Oregon-R-modENCODE [ALL]
head [ALL]
embargo expired
GBrowse tracks: submission_5363.sorted
SRA: SRR488280


3 files Download data files