Populus RNA-seq and ChIP-seq
Data and Software

P. Trichocarpa Since 2011 together with Dr. Andrew Groover at the US Forest Service and our students and colleagues: Llijun Liu, Matt Zinkgraf, Trevor Ramsay, Victor Missirian, and Suzane Gertulla, we have been working on deciphering key gene regulatory relationships effecting secondary tree growth in poplar trees. We are grateful to the USDA AFRI (grant 2011-67013-30062) for their support of this project. This page is dedicated to the software we and others have written and a virtual machine we have compiled for running the studies reported in our publications.

Virtual Machine

We have put together a virtual machine, available for download here, VM. It comprises of all the necessary software to be able to reproduce the results from our publications below. We have also uploaded it into iPlant, under the name Populus_ChIPseq_VM_1.0 .


This README file (pdf) gives the details of which software is installed on the virtual machine and how to use it.

Data Processing Scripts

The scripts we used to process the data are available here, and are described in the above README file.

Our Publications

ARK1 Network A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth in Populus
Lijun Liu, Trevor Ramsay, Matthew Zinkgraf, David Sundell, Nathaniel Robert Street, Vladimir Filkov, and Andrew Groover
Under review

The Populus ARBORKNOX1 homeobox transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function
Lijun Liu, Matthew Zinkgraf, H. Earl Petzold, Eric P. Beers, Vladimir Filkov, and Andrew Groover
New Phytologist, 205(2): 682-694, 2015

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Lijun Liu, Victor Missirian, Matthew Zinkgraf, Andrew Groover and Vladimir Filkov
BMC Genomics,2014, 15(Suppl 5):S3

Modeling transcriptional networks regulating secondary growth and wood formation in forest trees
Lijun Liu, Vladimir Filkov, Andrew Groover
Physiologia Plantarum, 2013, 151(2), 156 - 163