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RNAi of non-Histone Chromosomal Proteins in D. melanogaster

experiment: RNAi of non-Histone Chromosomal Proteins in D. melanogaster project: Chromosomal Proteins PI: Gary Karpen Labs: Sarah Elgin, Vincent Pirrotta
The goal of these experiments are to validate and confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. To do this, we are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, and then using antibodies to perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions.

All features generated by this experiment:
Feature Export
BindingSite 112797
This represents 100199 unique BindingSites 		TAB CSV GFF3 (for UCSC) SEQ
DepletedRegion 41073
This represents 34715 unique DepletedRegions 		TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All entries in public repositories generated by this experiment
There are 33 ChIP-chip, RNAi submissions for this experiment:
DCC id Name antibody RNAi reagent cell line Embargoed until Features, GBrowse and Data Files
modENCODE_3670

 CP190-HB.BG3.SU(HW) RNAi CP190-HB [ALL]
target: Centrosomal protein 190kD
 CG8573 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4532   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 87   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CP190-HB.BG3.SU_HW_RNAi
GEO: GSM811954
GEO: GSM811955
GEO: GSM811956
GEO: GSM811957


8 files Download data files
modENCODE_3671

 CTCF-VC.BG3.CP190 RNAi CTCF-VC [ALL]
target: CTCF
 CP190-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 1404   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 76   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CTCF-VC.BG3.CP190_RNAi
GEO: GSM811958
GEO: GSM811959
GEO: GSM811960
GEO: GSM811961


8 files Download data files
modENCODE_3673

 CTCF-VC.BG3.LacZ RNAi CTCF-VC [ALL]
target: CTCF
 LacZ-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 2876   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 1241   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CTCF-VC.BG3.LacZ_RNAi
GEO: GSM811968
GEO: GSM811969
GEO: GSM811970
GEO: GSM811971


8 files Download data files
modENCODE_3672

 CTCF-VC.BG3.CTCF RNAi CTCF-VC [ALL]
target: CTCF
 CTCF-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 628   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 125   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CTCF-VC.BG3.CTCF_RNAi
GEO: GSM811962
GEO: GSM811963
GEO: GSM811964
GEO: GSM811965
GEO: GSM811966
...All entries in public repositories generated by this submission



11 files Download data files
modENCODE_3666

 CP190-HB.BG3.BEAF RNAi CP190-HB [ALL]
target: Centrosomal protein 190kD
 CG10159_RNAi&oldid=39153 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4286   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 276   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CP190-HB.BG3.BEAF_RNAi
GEO: GSM811936
GEO: GSM811937
GEO: GSM811938
GEO: GSM811939


8 files Download data files
modENCODE_3667

 CP190-HB.BG3.CTCF RNAi CP190-HB [ALL]
target: Centrosomal protein 190kD
 CTCF-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4869   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 496   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CP190-HB.BG3.CTCF_RNAi
GEO: GSM811940
GEO: GSM811941
GEO: GSM811942
GEO: GSM811943


8 files Download data files
modENCODE_3669

 CP190-HB.BG3.mod RNAi CP190-HB [ALL]
target: Centrosomal protein 190kD
 MOD(MDG4)_all-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 6403   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 335   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CP190-HB.BG3.mod_RNAi
GEO: GSM811950
GEO: GSM811951
GEO: GSM811952
GEO: GSM811953


8 files Download data files
modENCODE_3668

 CP190-HB.BG3.LacZ RNAi CP190-HB [ALL]
target: Centrosomal protein 190kD
 LacZ-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 6363   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 1524   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CP190-HB.BG3.LacZ_RNAi
GEO: GSM811944
GEO: GSM811945
GEO: GSM811946
GEO: GSM811947
GEO: GSM811948
...All entries in public repositories generated by this submission



11 files Download data files
modENCODE_3663

 BEAF-HB.BG3.BEAF RNAi BEAF-HB [ALL]
target: Boundary element-associated factor of 32kD
 CG10159_RNAi&oldid=39153 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 1680   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 10   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: BEAF-HB.BG3.BEAF_RNAi
GEO: GSM811924
GEO: GSM811925
GEO: GSM811926
GEO: GSM811927


8 files Download data files
modENCODE_3707

 HP1 wa191.S2.GFP RNAi HP1 wa191 [ALL]
target: Suppressor of variegation 205
 GFP [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 1798   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 808   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: HP1wa191.S2.GFP_RNAi
GEO: GSM812044
GEO: GSM812045
GEO: GSM812046
GEO: GSM812047


8 files Download data files
modENCODE_3664

 BEAF-HB.BG3.CP190 RNAi BEAF-HB [ALL]
target: Boundary element-associated factor of 32kD
 CP190-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 3192   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 93   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: BEAF-HB.BG3.CP190_RNAi
GEO: GSM811928
GEO: GSM811929
GEO: GSM811930
GEO: GSM811931


8 files Download data files
modENCODE_3665

 BEAF-HB.BG3.LacZ RNAi BEAF-HB [ALL]
target: Boundary element-associated factor of 32kD
 LacZ-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4299   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 87   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: BEAF-HB.BG3.LacZ_RNAi
GEO: GSM811932
GEO: GSM811933
GEO: GSM811934
GEO: GSM811935


8 files Download data files
modENCODE_3893

 HP1 wa191.S2.HP1a RNAi HP1 wa191 [ALL]
target: Suppressor of variegation 205
 HP1a-RNAi [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 908   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 47   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: HP1wa191.S2.HP1a_RNAi
GEO: GSM812276
GEO: GSM812277
GEO: GSM812278
GEO: GSM812279


8 files Download data files
modENCODE_3537

 H3K4me3 (ab8580 lot1).BG3.CTCF RNAi H3K4me3 (ab8580 lot1) [ALL] /
target: H3K4me3
CTCF-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4893   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 2946   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K4me3_ab8580lot1.BG3.CTCF_RNAi
GEO: GSM811920
GEO: GSM811921
GEO: GSM811922
GEO: GSM811923


8 files Download data files
modENCODE_3583

 H3K4me3 (ab8580 lot1).BG3.CTCF RNAi H3K4me3 (ab8580 lot1) [ALL] /
target: H3K4me3
CTCF-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4867   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 2966   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K4me3.ab8580lot1.BG3.CTCF_RNAi
GEO: GSM1256126
GEO: GSM1256127
GEO: GSM1256128
GEO: GSM1256129


8 files Download data files
modENCODE_3712

 RNA Pol II (abcam).S2.Egg RNAi RNA Pol II (abcam) [ALL]
target: RNA polymerase II 215kD subunit
 EGG-RNAi [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 3172   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 86   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: RNAPolII_abcam.S2.Egg_RNAi
GEO: GSM812060
GEO: GSM812061
GEO: GSM812062
GEO: GSM812063


8 files Download data files
modENCODE_3680

 H3K27Me3 (Abcam2).BG3.CP190 RNAi H3K27Me3 (Abcam2) [ALL]
target: His3:CG33803
 CP190-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 3849   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 3007   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K27Me3_Abcam2.BG3.CP190_RNAi
GEO: GSM811992
GEO: GSM811993
GEO: GSM811994
GEO: GSM811995


8 files Download data files
modENCODE_3713

 RNA Pol II (abcam).S2.GFP RNAi RNA Pol II (abcam) [ALL]
target: RNA polymerase II 215kD subunit
 GFP [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 3706   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 198   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: RNAPolII_abcam.S2.GFP_RNAi
GEO: GSM812064
GEO: GSM812065
GEO: GSM812066
GEO: GSM812067


8 files Download data files
modENCODE_3679

 H3K27Me3 (Abcam2).BG3.BEAF RNAi H3K27Me3 (Abcam2) [ALL]
target: His3:CG33803
 CG10159_RNAi&oldid=39153 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 3885   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 3291   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K27Me3_Abcam2.BG3.BEAF_RNAi
GEO: GSM811988
GEO: GSM811989
GEO: GSM811990
GEO: GSM811991


8 files Download data files
modENCODE_3715

 SU(HW)-HB.BG3.CTCF RNAi SU(HW)-HB [ALL]
target: suppressor of Hairy wing
 CTCF-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4254   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 2044   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: SU_HW-HB.BG3.CTCF_RNAi
GEO: GSM812072
GEO: GSM812073
GEO: GSM812074
GEO: GSM812075


8 files Download data files
modENCODE_5600

 HP4 Q4072.S2.HP4 RNAi HP4 Q4072 [ALL]
target: Heterochromatin protein 4
 S2-DRSC_CG8044 [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 70   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 149   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: HP4_Q4072.S2.HP4_RNAi
GEO: GSM1113929
GEO: GSM1113930
GEO: GSM1113931
GEO: GSM1113932


8 files Download data files
modENCODE_3674

 CTCF-VC.BG3.SU(HW) RNAi CTCF-VC [ALL]
target: CTCF
 CG8573 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 2006   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 335   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CTCF-VC.BG3.SU_HW_RNAi
GEO: GSM811972
GEO: GSM811973
GEO: GSM811974
GEO: GSM811975


8 files Download data files
modENCODE_3714

 SU(HW)-HB.BG3.CP190 RNAi SU(HW)-HB [ALL]
target: suppressor of Hairy wing
 CP190-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4033   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 683   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: SU_HW-HB.BG3.CP190_RNAi
GEO: GSM812068
GEO: GSM812069
GEO: GSM812070
GEO: GSM812071


8 files Download data files
modENCODE_3717

 SU(HW)-HB.BG3.mod RNAi SU(HW)-HB [ALL]
target: suppressor of Hairy wing
 MOD(MDG4)_all-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4472   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 942   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: SU_HW-HB.BG3.mod_RNAi
GEO: GSM812080
GEO: GSM812081
GEO: GSM812082
GEO: GSM812083


8 files Download data files
modENCODE_3716

 SU(HW)-HB.BG3.LacZ RNAi SU(HW)-HB [ALL]
target: suppressor of Hairy wing
 LacZ-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4187   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 2282   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: SU_HW-HB.BG3.LacZ_RNAi
GEO: GSM812076
GEO: GSM812077
GEO: GSM812078
GEO: GSM812079


8 files Download data files
modENCODE_3719

 SU(HW)-HB.S2.LacZ RNAi SU(HW)-HB [ALL]
target: suppressor of Hairy wing
 LacZ-RNAi [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 4309   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 390   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: SU_HW-HB.S2.LacZ_RNAi
GEO: GSM812090
GEO: GSM812091
GEO: GSM812092
GEO: GSM812093


8 files Download data files
modENCODE_3718

 SU(HW)-HB.BG3.SU(HW) RNAi SU(HW)-HB [ALL]
target: suppressor of Hairy wing
 CG8573 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 2574   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 493   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: SU_HW-HB.BG3.SU_HW_RNAi
GEO: GSM812084
GEO: GSM812085
GEO: GSM812086
GEO: GSM812087
GEO: GSM812088
...All entries in public repositories generated by this submission



11 files Download data files
modENCODE_3682

 H3K27Me3 (Abcam2).BG3.LacZ RNAi H3K27Me3 (Abcam2) [ALL]
target: His3:CG33803
 LacZ-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 3901   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 4135   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K27Me3_Abcam2.BG3.LacZ_RNAi
GEO: GSM812000
GEO: GSM812001
GEO: GSM812002
GEO: GSM812003


8 files Download data files
modENCODE_3681

 H3K27Me3 (Abcam2).BG3.CTCF RNAi H3K27Me3 (Abcam2) [ALL]
target: His3:CG33803
 CTCF-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4095   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 4089   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K27Me3_Abcam2.BG3.CTCF_RNAi
GEO: GSM811996
GEO: GSM811997
GEO: GSM811998
GEO: GSM811999


8 files Download data files
modENCODE_3747

 CP190-HB.BG3.CP190 RNAi CP190-HB [ALL]
target: Centrosomal protein 190kD
 CP190-RNAi [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 939   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 28   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: CP190-HB.BG3.CP190_RNAi
GEO: GSM812102
GEO: GSM812103
GEO: GSM812104
GEO: GSM812105
GEO: GSM812106


10 files Download data files
modENCODE_3683

 H3K27Me3 (Abcam2).BG3.SU(HW) RNAi H3K27Me3 (Abcam2) [ALL]
target: His3:CG33803
 CG8573 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 4656   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 4740   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K27Me3_Abcam2.BG3.SU_HW_RNAi
GEO: GSM812004
GEO: GSM812005
GEO: GSM812006
GEO: GSM812007


8 files Download data files
modENCODE_3691

 H3K4me3 (ab8580 lot1).BG3.SU(HW) RNAi H3K4me3 (ab8580 lot1) [ALL] /
target: H3K4me3
CG8573 [ALL]
ML-DmBG3-c2 [ALL]
embargo expired
BindingSite: 5079   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 3021   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H3K4me3_ab8580lot1.BG3.SU_HW_RNAi
GEO: GSM812020
GEO: GSM812021
GEO: GSM812022
GEO: GSM812023


8 files Download data files
modENCODE_5147

 SU(HW)-HB.S2.SuHw RNAi SU(HW)-HB [ALL]
target: suppressor of Hairy wing
 SU(HW)-RNAi [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 612   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
DepletedRegion: 43   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: SU_HW_HB.S2.SuHw_RNAi
GEO: GSM1113925
GEO: GSM1113926
GEO: GSM1113927
GEO: GSM1113928


8 files Download data files




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Cambridge CB2 3EH, United Kingdom