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D melanogaster Small RNAs

experiment: D melanogaster Small RNAs project: The Drosophila Transcriptome PI: Sue Celniker Labs: Tom Gingeras
The cap-enriched and 5' monophosphate D. melanogaster small RNA libraries were generated in biological duplicate. Each library was mapped independently using STAR (Gingeras Lab) to the dm3 assembly without U-extra. To further assess the data we constructed contigs from the merged biological replciates and calculated Reads per Million values for every exon annotated in Flybase 5.32 and Ginormous. Additionally, we assessed each element for reproducibility using a nonparametric irreproducible detection rate script (npIDR, Alex Dobin Gingeras lab).

All features generated by this experiment:
Feature Export
Exon 3545493
This represents 85068 unique Exons
TAB CSV GFF3 (for UCSC) SEQ
Contig 1744979
This represents 1471500 unique Contigs
TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
There are 30 Computational annotation submissions for this experiment:
DCC id Name cell line compartment Embargoed until Features, GBrowse and Data Files
modENCODE_4324


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4211

Kc167 Nuclear CIP-TAP smallRNA-seq alignment and analysis Kc167 [ALL]
nucleus [ALL]
embargo expired
Exon: 132284   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 74408   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4324.sorted


9 files Download data files
modENCODE_4321


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4208

Kc167 Whole cell Untreated smallRNA-seq alignment and analysis Kc167 [ALL]
embargo expired
Exon: 164469   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 87556   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4321.sorted


9 files Download data files
modENCODE_4326


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4213

S2R+ Whole cell CIP-TAP smallRNA-seq alignment and analysis S2R+ [ALL]
embargo expired
Exon: 71333   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 29583   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4326.sorted


9 files Download data files
modENCODE_4323


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4210

Kc167 Cyto Untreated smallRNA-seq alignment and analysis Kc167 [ALL]
cytoplasm [ALL]
embargo expired
Exon: 147994   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 73382   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4323.sorted


9 files Download data files
modENCODE_4344


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4231

Cl.8 Whole cell CIP-TAP smallRNA-seq alignment and analysis CME W1 Cl.8+ [ALL]
embargo expired
Exon: 77596   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 34627   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4344.sorted


9 files Download data files
modENCODE_4343


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4230

BG3 Nuclear Untreated smallRNA-seq alignment and analysis ML-DmBG3-c2 [ALL]
nucleus [ALL]
embargo expired
Exon: 169153   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 90365   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4343.sorted


9 files Download data files
modENCODE_4346


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4233

Cl.8 Cyto CIP-TAP smallRNA-seq alignment and analysis CME W1 Cl.8+ [ALL]
cytoplasm [ALL]
embargo expired
Exon: 73849   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 30460   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4346.sorted


9 files Download data files
modENCODE_4345


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4232

Cl.8 Whole cell Untreated smallRNA-seq alignment and analysis CME W1 Cl.8+ [ALL]
embargo expired
Exon: 137726   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 75245   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4345.sorted


9 files Download data files
modENCODE_4334


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4221

S2-DRSC Cyto CIP-TAP smallRNA-seq alignment and analysis S2-DRSC [ALL]
cytoplasm [ALL]
embargo expired
Exon: 113597   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 50038   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4334.sorted


9 files Download data files
modENCODE_4331


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4218

S2R+ Nuclear Untreated smallRNA-seq alignment and analysis S2R+ [ALL]
nucleus [ALL]
embargo expired
Exon: 170120   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 96456   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4331.sorted


9 files Download data files
modENCODE_4328


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4215

S2R+ Cyto CIP-TAP smallRNA-seq alignment and analysis S2R+ [ALL]
cytoplasm [ALL]
embargo expired
Exon: 109663   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 39489   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4328.sorted


9 files Download data files
modENCODE_4333


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4220

S2-DRSC Whole cell Untreated smallRNA-seq alignment and analysis S2-DRSC [ALL]
embargo expired
Exon: 48102   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 16184   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4333.sorted


9 files Download data files
modENCODE_4322


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4209

Kc167 Cyto CIP-TAP smallRNA-seq alignment and analysis Kc167 [ALL]
cytoplasm [ALL]
embargo expired
Exon: 107238   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 35374   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4322.sorted


9 files Download data files
modENCODE_4325


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4212

Kc167 Nuclear Untreated smallRNA-seq alignment and analysis Kc167 [ALL]
nucleus [ALL]
embargo expired
Exon: 165376   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 97892   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4325.sorted


9 files Download data files
modENCODE_4332


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4219

S2-DRSC Whole cell CIP-TAP smallRNA-seq alignment and analysis S2-DRSC [ALL]
embargo expired
Exon: 113360   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 54409   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4332.sorted


9 files Download data files
modENCODE_4320


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4207

Kc167 Whole cell CIP-TAP smallRNA-seq alignment and analysis Kc167 [ALL]
embargo expired
Exon: 93323   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 35654   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4320.sorted


9 files Download data files
modENCODE_4339


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4226

BG3 Whole cell Untreated smallRNA-seq alignment and analysis ML-DmBG3-c2 [ALL]
embargo expired
Exon: 128979   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 65717   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4339.sorted


9 files Download data files
modENCODE_4340


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4227

BG3 Cyto CIP-TAP smallRNA-seq alignment and analysis ML-DmBG3-c2 [ALL]
cytoplasm [ALL]
embargo expired
Exon: 74111   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 25286   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4340.sorted


9 files Download data files
modENCODE_4341


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4228

BG3 Cyto Untreated smallRNA-seq alignment and analysis ML-DmBG3-c2 [ALL]
cytoplasm [ALL]
embargo expired
Exon: 130144   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 58015   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4341.sorted


9 files Download data files
modENCODE_4342


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4229

BG3 Nuclear CIP-TAP smallRNA-seq alignment and analysis ML-DmBG3-c2 [ALL]
nucleus [ALL]
embargo expired
Exon: 109523   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 44173   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4342.sorted


9 files Download data files
modENCODE_4347


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4234

Cl.8 Cyto Untreated smallRNA-seq alignment and analysis CME W1 Cl.8+ [ALL]
cytoplasm [ALL]
embargo expired
Exon: 127101   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 57712   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4347.sorted


9 files Download data files
modENCODE_4348


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4235

Cl.8 Nuclear CIP-TAP smallRNA-seq alignment and analysis CME W1 Cl.8+ [ALL]
nucleus [ALL]
embargo expired
Exon: 123277   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 64541   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4348.sorted


9 files Download data files
modENCODE_4349


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4236

Cl.8 Nuclear Untreated smallRNA-seq alignment and analysis CME W1 Cl.8+ [ALL]
nucleus [ALL]
embargo expired
Exon: 160249   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 105871   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4349.sorted


9 files Download data files
modENCODE_4335


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4222

S2-DRSC Cyto Untreated smallRNA-seq alignment and analysis S2-DRSC [ALL]
cytoplasm [ALL]
embargo expired
Exon: 84945   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 35722   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4335.sorted


9 files Download data files
modENCODE_4336


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4223

S2-DRSC Nuclear CIP-TAP smallRNA-seq alignment and analysis S2-DRSC [ALL]
nucleus [ALL]
embargo expired
Exon: 145604   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 84042   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4336.sorted


9 files Download data files
modENCODE_4337


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4224

S2-DRSC Nuclear Untreated smallRNA-seq alignment and analysis S2-DRSC [ALL]
nucleus [ALL]
embargo expired
Exon: 89085   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 40861   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4337.sorted


9 files Download data files
modENCODE_4338


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4225

BG3 Whole cell CIP-TAP smallRNA-seq alignment and analysis ML-DmBG3-c2 [ALL]
embargo expired
Exon: 62240   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 20178   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4338.sorted


9 files Download data files
modENCODE_4329


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3971
modENCODE_4216

S2R+ Cyto Untreated smallRNA-seq alignment and analysis S2R+ [ALL]
cytoplasm [ALL]
embargo expired
Exon: 156183   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 87308   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4329.sorted


9 files Download data files
modENCODE_4327


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3972
modENCODE_4214

S2R+ Whole cell Untreated smallRNA-seq alignment and analysis S2R+ [ALL]
embargo expired
Exon: 99831   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 61063   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4327.sorted


9 files Download data files
modENCODE_4330


Related to: modENCODE_2676
modENCODE_4057
modENCODE_3970
modENCODE_4217

S2R+ Nuclear CIP-TAP smallRNA-seq alignment and analysis S2R+ [ALL]
nucleus [ALL]
embargo expired
Exon: 159038   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Contig: 73368   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: submission_4330.sorted


9 files Download data files