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Identification of transcribed sequences under pathogenic bacterial growth conditions with expression profile maps

experiment: Identification of transcribed sequences under pathogenic bacterial growth conditions with expression profile maps project: The C. elegans Transcriptome PI: Robert Waterston Labs: Valerie Reinke
Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels. Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.

All features generated by this experiment:
Feature Export
TranscriptRegion ? 261696
This represents 163092 unique TranscriptRegions
TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All 12 tracks I II III IV V X
There are 6 tiling array: RNA submissions for this experiment:
DCC id Name developmental stage exposure time food strain Embargoed until Features, GBrowse and Data Files
modENCODE_486

pathogen Pluminscens 25dC 24hr exposure post-adulthood N2 tiling array Young Adult [ALL]
24 hours [ALL]
P. luminescens (Hb) [ALL]
N2 [ALL]
embargo expired
? TranscriptRegion: 44675   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: Hb_24
Hb_24


8 files Download data files
modENCODE_491

pathogen control OP50 25dC 24hr exposure post-adulthood N2 tiling array Young Adult [ALL]
24 hours [ALL]
E. coli (OP50) [ALL]
N2 [ALL]
embargo expired
? TranscriptRegion: 43626   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: OP50_24h
OP50_24h


8 files Download data files
modENCODE_489

pathogen Smarcescens 25dC 24hr exposure post-adulthood N2 tiling array Young Adult [ALL]
24 hours [ALL]
S. marcescens (Db11) [ALL]
N2 [ALL]
embargo expired
? TranscriptRegion: 42576   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: Db_24h
Db_24h


8 files Download data files
modENCODE_490

pathogen control OP50 25dC 48hr exposure post-adulthood N2 tiling array Young Adult [ALL]
48 hours [ALL]
E. coli (OP50) [ALL]
N2 [ALL]
embargo expired
? TranscriptRegion: 42590   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: OP50_48h
OP50_48h


8 files Download data files
modENCODE_488

pathogen Smarcescens 25dC 48hr exposure post-adulthood N2 tiling array Young Adult [ALL]
48 hours [ALL]
S. marcescens (Db11) [ALL]
N2 [ALL]
embargo expired
? TranscriptRegion: 45166   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: Db_48h
Db_48h


8 files Download data files
modENCODE_487

pathogen Efaecalis 25dC 24hr exposure post-adulthood N2 tiling array Young Adult [ALL]
24 hours [ALL]
E. faecalis (OG1RF) [ALL]
N2 [ALL]
embargo expired
? TranscriptRegion: 43063   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: OG1RF_24h
OG1RF_24h


6 files Download data files