SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

[1]  Xu Peng,et al.  A comparative study of ChIP-seq sequencing library preparation methods , 2016, BMC Genomics.

[2]  F. van Nieuwerburgh,et al.  Library construction for next-generation sequencing: overviews and challenges. , 2014, BioTechniques.

[3]  V. Cheung,et al.  RNA–DNA sequence differences in Saccharomyces cerevisiae , 2016, Genome research.

[4]  S. Henikoff,et al.  An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites , 2016, bioRxiv.

[5]  Alon Goren,et al.  Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences , 2017, PloS one.

[6]  John Quackenbush,et al.  What would you do if you could sequence everything? , 2008, Nature Biotechnology.

[7]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[8]  J. L. Mateo,et al.  Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal , 2015, Genome research.

[9]  David Haussler,et al.  The UCSC Genome Browser database: 2018 update , 2017, Nucleic Acids Res..

[10]  G. Gilfillan,et al.  How low can you go? Pushing the limits of low-input ChIP-seq. , 2018, Briefings in functional genomics.

[11]  R. Sandberg,et al.  Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells , 2012, Nature Biotechnology.

[12]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[13]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[14]  P. Lichter,et al.  Capture and Amplification by Tailing and Switching (CATS) , 2014, RNA biology.

[15]  R. Myers,et al.  Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. , 2005, Genome research.

[16]  Yong Zhang,et al.  Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos , 2016, Nature.

[17]  Piero Carninci,et al.  Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching , 2012, Nucleic acids research.

[18]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[19]  Thean-Hock Tang,et al.  Biases in small RNA deep sequencing data , 2013, Nucleic acids research.

[20]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[21]  Tao Ye,et al.  seqMINER: an integrated ChIP-seq data interpretation platform , 2010, Nucleic acids research.

[22]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[23]  Erez Lieberman Aiden,et al.  The expanding scope of DNA sequencing , 2012, Nature Biotechnology.

[24]  A. Sharrocks The ETS-domain transcription factor family , 2001, Nature Reviews Molecular Cell Biology.

[25]  Shan Zong,et al.  Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination , 2015, PLoS genetics.

[26]  James S. Duncan,et al.  Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex. , 2017, Cancer discovery.

[27]  G. Hannon,et al.  BPTF Maintains Chromatin Accessibility and the Self-Renewal Capacity of Mammary Gland Stem Cells , 2017, Stem cell reports.

[28]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[29]  Mustafa Tekin,et al.  Next generation sequencing: implications in personalized medicine and pharmacogenomics. , 2016, Molecular bioSystems.

[30]  Peiyong Jiang,et al.  Single-Stranded DNA Library Preparation Preferentially Enriches Short Maternal DNA in Maternal Plasma. , 2017, Clinical chemistry.

[31]  C. Thermes,et al.  Library preparation methods for next-generation sequencing: tone down the bias. , 2014, Experimental cell research.

[32]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[33]  J. McPherson,et al.  Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.