LI Ng gIF ChIP Track Settings
 
Ludwig Institute/UCSD ChIP/Chip NimbleGen - Gamma Interferon Experiments   (All ENCODE Chromatin Immunoprecipitation tracks)

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 Configure 		 LI Ng H3K4m3 -gIF  Ludwig Institute/UCSD ChIP/Chip Ng: HeLa, H3K4me3, no gamma interferon   Data format 
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 Configure 		 LI Ng H3K4m3 +gIF  Ludwig Institute/UCSD ChIP/Chip Ng: HeLa, H3K4me3, 30 min after gamma interferon   Data format 
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 Configure 		 LI Ng Pol2 -gIF  Ludwig Institute/UCSD ChIP/Chip Ng: HeLa, Pol2, no gamma interferon   Data format 
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 Configure 		 LI Ng Pol2 +gIF  Ludwig Institute/UCSD ChIP/Chip Ng: HeLa, Pol2, 30 min after gamma interferon   Data format 
Source data version: ENCODE June 2005 Freeze
Assembly: Human July 2003 (NCBI34/hg16)
Data coordinates converted via liftOver from: May 2004 (NCBI35/hg17)

Description

This track displays results of the following ChIP-chip (NimbleGen) gamma interferon experiments on HeLa cells:

  • anti-H3K4me3, no gamma interferon
  • anti-H3K4me3, 30 minutes after gamma interferon
  • anti-RNA Pol2 in initiation complex, no gamma interferon
  • anti-RNA Pol2 in initiation complex, 30 minutes after gamma interferon

ENCODE region-wide location analysis of trimethylated K4 histone H3 (H3K4me3, or triMeH3K4) and RNA polymerase II was conducted with ChIP-chip using chromatin extracted from HeLa cells induced for 30 minutes with gamma interferon as well as uninduced cells.

Methods

Chromatin from both induced and uninduced HeLa cells was separately cross-linked, precipitated with different antibodies, sheared, amplified and hybridized to an oligonucleotide tiling array produced by NimbleGen Systems. The array includes non-repetitive sequences within the 44 ENCODE regions tiled from NCBI Build 35 (UCSC hg17) with 50-mer probes at 38 bp interval. Resulting genomic coordinates were translated to NCBI Build 34 (UCSC hg16).

Intensity values for biological replicate arrays were combined after quantile normalization using R. The averages of the quantile normalized intensity values for each probe were then median-scaled and loess-normalized using R to obtain the adjusted log R values.

Verification

Three biological replicates were used to generate the track for each factor at each time point with the exception of RNA Pol2 uninduced, for which only two biological replicates were used.

Credits

The data for this track were generated at the Ren Lab, Ludwig Institute for Cancer Research at UC San Diego.