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RNAi of Histone Proteins in D. melanogaster

experiment: RNAi of Histone Proteins in D. melanogaster project: Chromosomal Proteins PI: Gary Karpen Labs: Gary Karpen
The goal of these experiments are to a) validate/confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome and b) evaluate their biological significance by assaying the impact of depletion on other proteins/marks. We are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, followed by Chromatin ImmunoPrecipitation (ChIP) assayed on 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 29089 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 2 ChIP-seq submissions for this experiment:
DCC id Name antibody RNAi reagent cell line Embargoed until Features, GBrowse and Data Files
modENCODE_5596

H2AV-9751.S2.GFP RNAi.Solexa H2AV_9751 [ALL]
target: Histone H2A variant
GFP [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 12967   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
repset.20448085.enrichment.clusters.gff3: 4698   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
2579.enrichment.clusters.gff3: 4071   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
2577.enrichment.clusters.gff3: 4198   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H2AV_9751_S2_GFP_RNAi
GEO: GSM1256873
GEO: GSM1256874
GEO: GSM1256875
GEO: GSM1256876


7 files Download data files
modENCODE_5595

H2AV-9751.S2.H2AV RNAi.Solexa H2AV_9751 [ALL]
target: Histone H2A variant
H2AV [ALL]
S2-DRSC [ALL]
embargo expired
BindingSite: 16122   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
2576.enrichment.clusters.gff3: 5019   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
2578.enrichment.clusters.gff3: 5037   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
repset.20448084.enrichment.clusters.gff3: 6066   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: H2AV_9751_S2_H2AV_RNAi
GEO: GSM1256869
GEO: GSM1256870
GEO: GSM1256871
GEO: GSM1256872


7 files Download data files