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Table of Contents

tree-hmm sample .bam's from chr19

tree-hmm sample data from the ENCODE human project http://cbcl.ics.uci.edu/public_data/tree-hmm-sample-data

LRH-1 ChIP-seq Data

Our ChIP-seq analysis of LRH-1 can be found at: http://cbcl.ics.uci.edu/public_data/LRH-1

FXR ChIP-seq Data

http://cbcl.ics.uci.edu/public_data/FXR/

SREBP-2 ChIP-seq Data

ChipSeq was performed on SREBP-2 and peaks were called using GLITR. We also re-analyzed SREBP-1 using GLITR. Supplemental Tables, Figures, and datasets are available: SREBP2

SREBP-1 ChIP-seq Data

Included here is ChIP-Seq raw and processed data from:

Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. PNAS 2009 106:13765-13769; Young-Kyo Seo, Hansook Kim Chong, Aniello M. Infante, Seung-Soon Im, Xiaohui Xie, and Timothy F. Osborne

  • Raw sequence data (raw_data/*_sequence.txt) was processed using eland to create raw/*_eland_multi.txt
  • ChipSeq-mini 2.0 (http://woldlab.caltech.edu/html/software, now part of the ERANGE package) was used to process the eland files and produce the processed/*.bed files.
  • IgG files are for the control run, SREBP1 files are after fasting and refeeding. See paper for details.
  1. Processed Data
  2. Raw Data
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