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ABBREVIATIONS
ADT
Androgen-Deprivation Therapy
CRPC
Castration Resistant Prostate Cancer
ChIP-seq
Chromatin Immunoprecipitation followed by Sequencing
ENCODE
The Encyclopedia of DNA Elements Project
FACS
Fluorescence-Activated Cell Sorting
GEO
Gene Expression Omnibus
GSEA
Gene Set Enrichment Analysis
H3K4me1
Histone 3 Lysine 4 Mono-methylation
H3K4me3
Histone 3 Lysine 4 Tri-methylation
H3K36me3 Histone 3 Lysine 36 Tri-methylation
H3K9ac
Histone 3 Lysine 9 Acetylation
H3K27me3 Histone 3 Lysine 27 Tri-methylation
H3K9me3
Histone 3 Lysine 9 Tri-methylation
NGS
Next Generation Sequencing
PCSC
Prostate Cancer Stem Cell
PSA
Prostate Specific Antigen
SVM
Support Vector Machines
TCGA
The Cancer Genome Atlas
FACILITIES and RESOURCES
We have full access to high performance computer cluster in Dan L. Duncan Cancer
Center, which is equipped with 26 computation nodes, including 18 nodes with two 4core AMD 2312 CPUs and 32GB memory each node, and 8 high performance nodes with
two 6-core Intel Xeon 5690 CPUs and 96GB memory. These node share 30 TB hard disk
storage with distributed backup system. We also have access to BlueBioU super
computer in Rice University as secondary computation resource. The BlueBiou computer
cluster contain 47 nodes with four 8-core POWER7 CPUs and 256GB memory each
node, and share a total 474TB (217TB BlueBiou specific and 257 TB common) storage
system. (http://www.rcsg.rice.edu/sharecore/bluebiou/)
The Human Genome Sequencing Center (HGSC) at Baylor College of Medicine (BCM)
will provide sequencing service for ChIP-seq. BCM-HGSC is equipped with Illumina
Solexa Hiseq 2000 sequencing system for high throughput next generation sequencing.
PUBLICATIONS
1. Yao J, Liu X, Sakuno T, Li W, Xi Y, Aravamudhan P, Joglekar A, Li W, Watanabe Y, He X:
Plasticity and Epigenetic Inheritance of Centromere Specific Histone H3 (CENP-A)
Containing-Nucleosome Positioning in the Fission Yeast. J Biol Chem. 2013;
288(26):19184-96. PMID: 23661703
2. Chen K, Xi Y, Pan X, Dent S, He X, Li W: DANPOS: Dynamic Analysis of Nucleosome
Position and Occupancy by Sequencing. Genome Res. 2013; 23(2):341-51. PMID: 23193179
3. MF Barber*, Michishita E*, Xi Y*(joint first author), Tasselli L, Kioi M, Moqtaderi Z,
Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W, Chua KF.
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature.
2012; 487(7405), 114–118. PMID: 22722849
4. Xiao R, Sun D, Dayers S, Xi Y, Li W, Moore D. The Estrogen Receptor Alpha Cistrome
Defined by DamIP. Mol Endocrinol. 2012;26(2):349-357. PMID: 22207717
5. Klisch TJ*, Xi Y*(joint first author), Flora A, Wang L, Li W, Zoghbi HY. In vivo Atoh1
targetome reveals how a proneural transcription factor regulates cerebellar development. Proc
Natl Acad Sci USA. 2011 108(8):3288-3293. PMID: 21300888
6. Xi Y*, Bock C*, Müller F, Sun D, Meissner A, Li W. RRBSMAP: A Fast, Accurate and
User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing.
Bioinformatics. 2012;28(3):430-432. PMID: 22155871
7. Challen G, Sun D, Jeong M, Luo M, Jelinek J, Berg J, Bock C, Vasanthakumar A, Gu H, Xi
Y, Liang S, Lu Y, Darlington G, Meissner A, Issa J, Godley L, Li W, Goodell M. Dnmt3a is
Essential for Hematopoietic Stem Cell Differentiation. Nat Genet. 2011; 44(1):23-31. PMID:
22138693
8. Xi Y*, Yao J*, Chen R, Li W, He X. Nucleosome fragility reveals novel functional states of
chromatin and poises genes for activation. Genome Res. 2011; 21(5):718-724. PMID:
21363969
9. Xi Y, Li W. BSMAP: whole genome bisulfite sequence mapping program. BMC
Bioinformatics. 2009; 10:232. PMID: 19635165
10. Kuo AJ, Cheung P, Chen K, Zee BM, Kioi M, Lauring J, Xi Y, Park BH, Shi X, Garcia BA,
Li W, Gozani O. NSD2 Links Dimethylation of Histone H3 at Lysine 36 to Oncogenic
Programming. Mol Cell. 2011; 44(4):609-620
11. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD,
Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen
H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY,
Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland
RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of
sequencing-based methods to profile DNA methylation and identification of monoallelic
epigenetic modifications. Nat Biotechnol. 2010; 28(10):1097-1105. PMID: 20852635
12. Kim BJ, Li Y, Zhang J, Xi Y, Li Y, Yang T, Jung SY, Pan X, Chen R, Li W, Wang Y, Qin J.
Genome-wide reinforcement of cohesin binding at pre-existing cohesin sites in response to
ionizing radiation in human cells. J Biol Chem. 2010; 285(30):22784-22792. PMID:
20501661
13. Xi Y, de Ropp JS, Viant MR, Woodruff DL, Yu P. Improved identification of metabolites in
complex mixtures using HSQC NMR spectroscopy. Anal Chim Acta. 2008; 614(2):127-133.
PMID: 18420042
14. Xi Y, Rocke DM. Baseline correction for NMR spectroscopic metabolomics data analysis.
BMC Bioinformatics. 2008; 9:324. PMID: 18664284
15. Xi Y, de Ropp J, Viant M, Woodruff D, Yu P. Automated screening for metabolites in
complex mixtures using 2D COSY NMR spectroscopy. Metabolomics, 2006; 2(4): 221-233.
INTELLECTUAL PROPERTY PLAN
The results of the proposed study will be published in peered reviewed journals. The data
processing pipeline, including the source code and manual, will be released for public usage
without charges under the GNU General Public License version 3 (GPLv3)
(http://www.gnu.org/licenses/agpl-3.0.html)
DATA AND RESEARCH RESOURCE SHARING PLAN
The ChIP-seq raw reads and processed data will be deposited to the NCBI Gene Expression
Omnibus (GEO) database. (http://www.ncbi.nlm.nih.gov/geo/) We also plan to build a
customized website to host the data, software, publications and analyses results of the proposed
study for public access.