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scforest.tex
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\documentclass[12pt, a4]{article}
\usepackage[utf8]{inputenc}
\usepackage[euler]{textgreek}
\usepackage{amsmath}
\DeclareMathSizes{12}{30}{16}{12}
\usepackage{tikz}
\usetikzlibrary{arrows.meta}
\usetikzlibrary{decorations.pathmorphing}
\usetikzlibrary{backgrounds,fit}
\usetikzlibrary{decorations.pathreplacing,angles,quotes}
\usepackage{tikz-qtree}
\usepackage{forest}
\usepackage{natbib}
\usepackage[pdfusetitle,hidelinks,plainpages=false]{hyperref}
\hypersetup{
colorlinks=true,
urlcolor=.,
citecolor=.
}
\usepackage{lscape}
\usepackage[a4paper]{geometry}
\title{scforest}
\author{Florian De Rop}
\date{\today}
\begin{document}
\begin{titlepage}
\begin{center}
\vspace*{1cm}
{\huge\textbf{scforest}}
\vspace{0.5cm}
{\Large A visual overview of single cell technology}
\vspace{1.5cm}
{\large Curated by Florian De Rop}\\
\medskip
{\large \href{https://www.aertslab.org/}{Aerts Lab}}\\
\medskip
{\large \today}\\
\medskip
{\large Updated version on \href{https://github.com/aertslab/scforest}{github.com/aertslab/scforest}}\\
\vfill
\includegraphics[width=0.4\textwidth]{kuleuven.jpeg}\\
\medskip
KU Leuven/VIB\\
\end{center}
\end{titlepage}
\eject
\pdfpagewidth=210cm
\pdfpageheight=60cm
\newgeometry{layout=a0paper}
\forestset{sctree/.style={for tree={anchor=center, align=center, inner sep=0pt, edge=thick}}}
\forestset{
empty/.style={
for tree={calign=center},
delay={where content={}{shape=coordinate, for siblings={anchor=north}}{}}
},
}
\forestset{%
/tikz/squiggly/.style={-{Latex[length=2mm, width=1.5mm]}, decorate, decoration={snake, amplitude=0.5mm, segment length=4mm, post length=1mm}},
commercial/.style={edge=squiggly},
move me/.style n args=2{%
before drawing tree={%
x+=#1,
y+=#2,
},
},
}
\newpage
\begin{center}
\begin{forest}, sctree, calign=center
[, empty, calign=center
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[, empty, no edge, tier=base[, empty, no edge
[\textbf{\large{1992}}, no edge, name=1992l, tier=1992[, empty, no edge, tier=1992b
[\textbf{\large{2006}}, no edge, name=2006l, tier=2006[, empty, no edge, tier=2006b
[\textbf{\large{2007}}, no edge, tier=2007[, empty, no edge, tier=2007b
[\textbf{\large{2008}}, no edge, tier=2008[, empty, no edge, tier=2008b
[\textbf{\large{2009}}, no edge, tier=2009[, empty, no edge, tier=2009b
[\textbf{\large{2010}}, no edge, tier=2010[, empty, no edge, tier=2010b
[\textbf{\large{2011}}, no edge, tier=2011[, empty, no edge, tier=2011b
[\textbf{\large{2012}}, no edge, tier=2012[, empty, no edge, tier=2012b
[\textbf{\large{2013}}, no edge, tier=2013[, empty, no edge, tier=2013b
[\textbf{\large{2014}}, no edge, tier=2014[, empty, no edge, tier=2014b
[\textbf{\large{2015}}, no edge, tier=2015[, empty, no edge, tier=2015b
[\textbf{\large{2016}}, no edge, tier=2016[, empty, no edge, tier=2016b
[\textbf{\large{2017}}, no edge, tier=2017[, empty, no edge, tier=2017b
[\textbf{\large{2018}}, no edge, tier=2018[, empty, no edge, tier=2018b
[\textbf{\large{2019}}, no edge, tier=2019[, empty, no edge, tier=2019b
]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% proteomics
[, no edge, fit=band, tier=2019b, name=sep_proteomics]
[, empty, no edge, name=prereap-seq[\href{https://www.nature.com/articles/nbt.3973}{\textbf{REAP-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{peterson2017}, no edge, fit=tight, name=reap-seq, tier=2017
[\href{https://doi.org/10.1186/s13059-018-1547-5}{\textbf{SCoPE-MS}}\\\citealt{budnik2018}, no edge, fit=tight, name=scope-ms, tier=2018
[\href{http://dx.doi.org/10.1101/749473.}{\textbf{SPARC\textsuperscript{\textbf{\large{+}}}}}\\\citealt{reimegard2019}, no edge, fit=tight, name=sparc, tier=2019]
]
]]
[, empty, no edge, fit=band[\href{https://www.nature.com/articles/nmeth.4380}{\textbf{CITE-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{stoeckius2017}, no edge, fit=band, name=cite-seq, tier=2017
[, empty, no edge[\href{https://www.nature.com/articles/s41467-018-07115-y}{\textbf{Pi-ATAC\textsuperscript{\textbf{\large{+}}}}}\\\citealt{chen2018a}, no edge, fit=band, name=pi-atac, tier=2018]]
]]
[, empty, no edge, fit=band[\href{https://doi.org/10.1016/j.cell.2018.09.022}{\textbf{Pro-Code}}\\\citealt{wroblewska2018}, no edge, fit=band, name=pro-code, tier=2018
]]
% spatial transcriptomics
[, no edge, fit=band, tier=2019b, name=sep_transcriptomics]
[, no edge, calign=center, tier=base
[, empty, no edge[\href{https://science.sciencemag.org/content/348/6233/aaa6090}{\textbf{MERFISH\textsuperscript{\large{\textmu}}}}\\\citealt{chen2015}, no edge, fit=tight, tier=2015
[\href{https://www.nature.com/articles/s41598-018-22297-7}{\textbf{Expansion\textsuperscript{\large{\textmu}}}}\\\href{https://www.nature.com/articles/s41598-018-22297-7}{\textbf{MERFISH}}\\\citealt{wang2018a}, fit=tight, tier=2018
[\href{https://www.nature.com/articles/s41598-019-43943-8}{\textbf{Branched\textsuperscript{\large{\textmu}}}}\\\href{https://www.nature.com/articles/s41598-019-43943-8}{\textbf{MERFISH}}\\\citealt{xia2019}, fit=tight, tier=2019]
]
]]
[, empty, no edge[\href{https://science.sciencemag.org/content/353/6294/78}{\textbf{Spatial\textsuperscript{\large{\textmu}}}}\\\href{https://science.sciencemag.org/content/353/6294/78}{\textbf{Transcriptomics}}\\\citealt{stahl2016}, no edge, fit=band, name=spatial_transcriptomics, tier=2016
[\href{https://doi.org/10.1038/s41596-018-0045-2}{\textbf{Spatial\textsuperscript{\large{\textmu}}}}\\\href{https://doi.org/10.1038/s41596-018-0045-2}{\textbf{Transcriptomics}}\\\citealt{salmen2018}, fit=tight, tier=2018
[\href{https://www.nature.com/articles/s41592-019-0548-y}{\textbf{HDST\textsuperscript{\large{\textmu}}}}\\\citealt{vickovic2019}\\10x Genomics, commercial, fit=band, tier=2019]
]
]]
[, empty, no edge[\href{https://www.cell.com/neuron/fulltext/S0896-6273(16)30702-4}{\textbf{seqFISH\textsuperscript{\large{\textmu}}}}\\\citealt{shah2016}, no edge, fit=band, name=seqfish, tier=2016
[\href{https://www.nature.com/articles/s41586-019-1049-y}{\textbf{seqFISH+\textsuperscript{\large{\textmu}}}}\\\citealt{eng2019}, edge, fit=band, tier=2019]
]]
[, empty, no edge[\href{https://science.sciencemag.org/content/343/6177/1360.long}{\textbf{FISSEQ\textsuperscript{\large{\textmu}}}}\\\citealt{lee2014}, no edge, fit=band, tier=2014
[, empty[\href{https://www.nature.com/articles/nprot.2014.191}{\textbf{FISSEQ\textsuperscript{\large{\textmu}}}}\\\citealt{lee2015}, fit=band, tier=2015
[, empty, no edge[\href{https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpmb.44}{\textbf{subRNA-seq\textsuperscript{\large{\textmu}}}}\\\citealt{mayer2017}, no edge, fit=band, tier=2017
[, empty, no edge[\href{https://science.sciencemag.org/content/361/6400/eaat5691}{\textbf{STARmap\textsuperscript{\large{\textmu}}}}\\\citealt{wang2018b}, no edge, fit=band, name=starmap, tier=2018
[\href{https://science.sciencemag.org/content/363/6434/1463}{\textbf{Slide-seq\textsuperscript{\large{\textmu}}}}\\\citealt{rodriques2019}, no edge, fit=band, tier=2019]
]]
]]
]]
]]
[, no edge, fit=band, tier=2019b, name=sep_spatial_transcriptomics]
% transcriptomics
[, empty, no edge[\href{https://doi.org/10.1073/pnas.1319700110}{\textbf{Single Nucleus}}\\\href{https://doi.org/10.1073/pnas.1319700110}{\textbf{cDNA Sequencing}}\\\citealt{grindberg2013}, no edge, fit=tight, tier=2013
[\href{https://science.sciencemag.org/content/347/6222/1258367.figures-only}{\textbf{CytoSeq}}\\\citealt{fan2015a}, no edge, fit=tight, tier=2015
[\href{https://www.nature.com/articles/ncomms13182}{\textbf{MASC-seq}}\\\citealt{vickovic2016}, no edge, fit=band, tier=2016
[\href{https://doi.org/10.1038/nmeth.4145}{\textbf{MATQ-seq}}\\\citealt{sheng2017}, no edge, fit=band, tier=2017]
]
]
]]
[, empty, no edge[\href{https://doi.org/10.1038/nbt.3701}{\textbf{small-RNA-seq}}\\\citealt{faridani2016}, no edge, fit=tight, tier=2016
[\href{https://doi.org/10.1038/s41467-018-07981-6}{\textbf{miRNA-mRNA}}\\\href{https://doi.org/10.1038/s41467-018-07981-6}{\textbf{co-sequencing}}\\\citealt{wang2019}, edge=dotted, fit=tight, tier=2019]
]]
[\href{https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r31}{\textbf{Quartz-seq}}\\\citealt{sasagawa2013}, no edge, fit=tight, tier=2013
[, empty[\href{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1407-3}{\textbf{Quartz-seq2}}\\\citealt{sasagawa2018}, fit=tight, tier=2018]]
]
[\href{https://www.pnas.org/content/89/7/3010}{\textbf{Eberwine}}\\\citealt{eberwine1992}, no edge, fit=tight, tier=1992
[\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(12)00228-8}{\textbf{CEL-seq}}\\\citealt{hashimshony2012}, edge=dotted, fit=tight, calign=child, calign child=2, tier=2012
[, empty, edge=dotted[\href{https://science.sciencemag.org/content/343/6172/776}{\textbf{MARS-seq}}\\\citealt{jaitin2014}, edge=dotted, fit=tight, tier=2014
[, empty[\href{https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(16)31611-7}{\textbf{CRISP-seq}}\\\citealt{jaitin2016}, fit=tight, tier=2016
]]
[, empty[\href{https://www.nature.com/articles/s41596-019-0164-4}{\textbf{MARS-seq2.0}}\\\citealt{keren-shaul2019}, fit=tight, tier=2019]]
]]
[, empty[\href{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0938-8}{\textbf{CEL-seq2}}\\\citealt{hashimshony2016}, tier=2016]]
[, empty, edge=dotted, fit=tight[\textbf{inDrop}\\\citealt{klein2015}, edge=dotted, calign=child, calign child=2, name=indrop, tier=2015
[\textbf{inDrop}\\1CellBio 2016, commercial, fit=band, tier=2016]
[\href{https://www.nature.com/articles/nprot.2016.154}{\textbf{inDrop}}\\\citealt{zilionis2017}, fit=band, tier=2017
[\href{https://science.sciencemag.org/content/360/6385/176}{\textbf{SPLiT-seq}}\\\citealt{rosenberg2018}, no edge, fit=tight, tier=2018]
]
]]
]]
[, empty, no edge[\href{https://doi.org/10.1016/j.cell.2016.11.038}{\textbf{Perturb-seq}}\\\citealt{dixit2016}\\\citealt{adamson2016}, no edge, fit=tight, name=perturb-seq, tier=2016
[\href{https://doi.org/10.1101/791525 }{\textbf{In-Vivo}}\\\href{https://doi.org/10.1101/791525}{\textbf{Perturb-seq}}\\\citealt{jin2019}, edge=dotted, fit=tight, name=in-vivo_perturb-seq, tier=2019]
]]
[\href{https://academic.oup.com/nar/article/34/5/e42/1146394}{\textbf{scMicroarray}}\\\citealt{kurimoto2006}, no edge, fit=tight, tier=2006
[\href{https://www.nature.com/articles/nprot.2007.79}{\textbf{scMicroarray}}\\\citealt{kurimoto2007}, tier=2007
[\href{https://www.nature.com/articles/nmeth.1315}{\textbf{mRNA-seq}}\\\citealt{tang2009}, edge=dotted, calign=child, calign child=3, fit=tight, name=mrna-seq, tier=2009
[, empty, edge=dotted, tier=2011[\href{https://www.pnas.org/content/111/19/7048.long}{\textbf{Microfluidic}}\\\href{https://www.pnas.org/content/111/19/7048.long}
{\textbf{mRNA-seq}}\\\citealt{streets2014}, edge=dotted, fit=tight, tier=2014
[, empty, no edge[\textbf{Chromium}\\10x Genomics 2016, no edge, fit=tight, name=chromium2016, tier=2016
[, empty[\textbf{\href{https://www.nature.com/articles/ncomms14049}{Chromium}}\\\citealt{zheng2017}\\10x Genomics, fit=tight, name=chromium2017, tier=2017
[, empty, edge=dotted[\href{https://www.nature.com/articles/s41467-019-11049-4}{\textbf{RAGE-seq}}\\\citealt{singh2019}, edge=dotted, fit=tight, name=rage-seq, tier=2019]]
]]
]]
]]
[, empty, edge=dotted[\href{https://genome.cshlp.org/content/21/7/1160.long}{\textbf{STRT-seq}}\\\citealt{islam2011}, edge=dotted, fit=tight, name=strt-seq, tier=2011
[\href{https://www.nature.com/articles/nprot.2012.022}{\textbf{STRT-seq}}\\\citealt{islam2012}, fit=tight, calign=child, calign child=2, name=strt-seq2012, tier=2012
[, empty, edge=dotted[\href{https://www.biorxiv.org/content/10.1101/003236v1}{\textbf{SCRB-seq}}\\\citealt{soumillon2014}, edge=dotted, fit=tight, tier=2014
[, empty[\href{https://www.sciencedirect.com/science/article/pii/S1097276517300497}{\textbf{SCRB-seq}}\\\citealt{ziegenhain2017}, fit=tight, tier=2017
[, empty[\href{https://www.nature.com/articles/s41467-018-05347-6}{\textbf{mcSCRB-seq}}\\\citealt{bagnoli2018}, fit=tight, tier=2018]]
]]
]]
[, empty, no edge[\href{https://doi.org/10.1038/nmeth.2772}{\textbf{C1-STRT-seq}}\\\citealt{islam2013}\\Fluidigm, name=c1-strt-seq, no edge, fit=tight, tier=2013
[, empty[\href{https://www.nature.com/articles/s41598-017-16546-4}{\textbf{STRT-seq-2i}}\\\citealt{hochgerner2017}, fit=tight, tier=2017
[, empty, no edge[\href{https://doi.org/10.1038/s41467-018-02866-0}{\textbf{RamDA-seq}}\\\citealt{hayashi2018}, no edge, fit=tight, tier=2018]]
]]
]]
]
]]
[, empty, edge=dotted[\href{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0706-1}{\textbf{SUPeR-seq}}\\\citealt{fan2015b}, edge=dotted, fit=tight, tier=2015]]
[, empty[\href{https://www.nature.com/articles/nprot.2009.236}{\textbf{scRNA-seq}}\\\citealt{tang2010}, fit=tight, tier=2010]]
[, empty, edge=dotted, tier=2010[\href{https://www.nature.com/articles/nbt.2282}{\textbf{Smart-seq}}\\\citealt{ramskold2012}, edge=dotted, calign=child, calign child=2, name=smart-seq, tier=2012
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.2694}{\textbf{C1 scRNA-seq}}\\\citealt{wu2013}\\Fluidigm, no edge, fit=tight, name=c1_scrna-seq, tier=2013
[, empty, no edge[\href{https://www.nature.com/articles/nbt.2967}{\textbf{C1 scRNA-seq}}\\\citealt{pollen2014}\\Fluidigm, no edge, fit=tight, name=c1_scrna-seq2, tier=2014
[, empty, edge=dotted[\href{https://www.nature.com/articles/s41598-017-04426-w}{\textbf{SNS}}\\\citealt{lake2017b}, edge=dotted, fit=tight, name=sns, tier=2017]]
]]
]]
[, empty[\href{https://www.nature.com/articles/nmeth.2639}{\textbf{Smart-seq2}}\\\citealt{picelli2013}, calign=child, calign child=1, fit=tight, name=smart-seq2, tier=2013
[, empty[\href{https://www.nature.com/articles/nprot.2014.006}{\textbf{Smart-seq2}}\\\citealt{picelli2014}, calign=child, calign child=4, fit=tight, name=smart-seq22, tier=2014
[, empty, edge=dotted, tier=2015b[\href{https://www.cell.com/cell/fulltext/S0092-8674(18)30116-8}{\textbf{Microwell-Seq}}\\\citealt{han2018}, edge=dotted, fit=tight, tier=2018]]
[, empty, edge=dotted, tier=2016[\href{10.1101/gr.234807.118}{\textbf{Smart3-SEQ}}\\\citealt{foley2019}, edge=dotted, fit=tight, tier=2019]]
[, empty, edge=dotted, tier=2015b[\href{https://www.nature.com/articles/ncomms10220}{\textbf{Microfluidic}}\\\href{https://www.nature.com/articles/ncomms10220}{\textbf{Smart-Seq}}\\\citealt{kimmerling2016}, edge=dotted, fit=tight, tier=2016]]
[, empty, tier=2015b[\href{https://doi.org/10.1101/817924 }{\textbf{Smart-seq3}}\\\citealt{hagemann-jensen2019},fit=tight, tier=2019]]
[, empty, edge=dotted, tier=2015b[\href{https://doi.org/10.1038/ncomms12139}{\textbf{LCM-seq\textsuperscript{\large{\textmu}}}}\\\citealt{nichterwitz2016}, edge=dotted, fit=tight, tier=2016]]
[, empty, edge=dotted, tier=2015b[\href{https://www.nature.com/articles/nbt.4259}{\textbf{ScISOr-seq}}\\\citealt{gupta2018}, edge=dotted, fit=tight, tier=2018]]
[, empty, edge=dotted, fit=tight, name=prescslam-seq, tier=2015b[\href{https://www.nature.com/articles/s41586-019-1369-y}{\textbf{scSLAM-seq}}\\\citealt{erhard2019}, edge=dotted, fit=tight, name=scslam-seq, tier=2019]]
[, empty, edge=dotted, fit=tight, name=prediv-seq, tier=2015b[\href{https://science.sciencemag.org/content/353/6302/925.long}{\textbf{Div-seq/sNuc-seq}}\\\citealt{habib2016}, edge=dotted, fit=tight, name=div-seq, tier=2016
[, empty, fit=tight, name=predronc-seq[\href{https://www.nature.com/articles/nmeth.4407}{\textbf{DroNC-seq}}\\\citealt{habib2017}, fit=tight, name=dronc-seq, tier=2017]]
]]
]]
[, empty, edge=dotted, fit=tight[\href{https://www.cell.com/abstract/S0092-8674(15)00549-8}{\textbf{Drop-seq}}\\\citealt{macosko2015}, edge=dotted, calign=child, calign child=2, fit=tight, name=drop-seq, tier=2015
[, empty, edge=dotted, tier=2016[\href{https://www.nature.com/articles/nmeth.4179}{\textbf{Seq-Well}}\\\citealt{gierahn2017}, edge=dotted, fit=tight, tier=2017
]]
[, empty, edge=dotted[\href{https://pubs.rsc.org/en/content/articlelanding/2019/lc/c9lc00014c}{\textbf{Simplified Drop-seq}}\\\citealt{biocanin2019}, edge=dotted, fit=tight, tier=2019]]
[, empty, edge=dotted, tier=2016[\href{https://www.nature.com/articles/nmeth.4177}{\textbf{CROP-seq}}\\\citealt{datlinger2017}, edge=dotted, fit=tight, tier=2017]]
[, empty, edge=dotted, tier=2016b[\href{https://www.sciencedirect.com/science/article/pii/S1097276517301740}{\textbf{Mosaic-seq}}\\\citealt{xie2017}, edge=dotted, fit=tight, name=mosaic-seq, tier=2017]]
[, empty, edge=dotted, tier=2016b[\href{https://www.nature.com/articles/nbt.4038}{\textbf{snDrop-seq}}\\\citealt{lake2017a}, edge=dotted, fit=tight, name=sndrop-seq, tier=2017]]
]]
]]
]]
]] % kurimoto papers
]
[, no edge, empty[\href{https://doi.org/10.1038/nmeth.1226}{\textbf{RNA-seq\textsuperscript{\textbf{\large{*}}}}}\\\citealt{mortazavi2008}, no edge, fit=tight, name=rna-seq, tier=2008]]
[, empty, no edge, tier=2013, name=prescirna-seq[\href{https://science.sciencemag.org/content/357/6352/661}{\textbf{sciRNA-seq}}\\\citealt{cao2017}, no edge, fit=band, name=scirna-seq, tier=2017]]
]
% multiomics
[, no edge, tier=2012, tier=base
[, empty, no edge, fit=band, name=sep_multiomics, tier=2019b]
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.3370}{\textbf{DR-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{dey2015}, no edge, fit=band, name=dr-seq, tier=2015, calign=child, calign child=1
[, empty, no edge, name=presnare-seq, tier=2017[\href{https://doi.org/10.1038/s41587-019-0290-0}{\textbf{SNARE-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{chen2019}, edge=dotted, fit=band, tier=2019]]
]]
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.3370}{\textbf{G{\&}T-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{macaulay2015}, no edge, fit=band, name=gt-seq, tier=2015, calign=child, calign child=1
[, empty[\href{https://www.nature.com/articles/nprot.2016.138}{\textbf{G{\&}T-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{macaulay2016}, fit=tight, tier=2016
[, empty, no edge, fit=band[\href{https://www.sciencedirect.com/science/article/abs/pii/S1097276519306185}{\textbf{sci-L3\textsuperscript{\textbf{\large{+}}}}}\\\citealt{yin2019}, no edge, fit=tight, name=sci-l3, tier=2019]]
]]
]]
[, empty, no edge[\href{https://www.sciencedirect.com/science/article/pii/S0027510715000044}{\textbf{SCTG\textsuperscript{\textbf{\large{+}}}}}\\\citealt{Li2015}, no edge, fit=tight, name=SCTG, tier=2015
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.3728}{\textbf{scM\&T-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{angermueller2016}, no edge, fit=tight, name=scmt-seq, tier=2016
[, empty[\href{https://www.nature.com/articles/s41467-018-03149-4}{\textbf{scNMT-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{clark2018}, fit=tight, name=scnmt-seq, tier=2018
[, empty, no edge[\href{https://www.nature.com/articles/s41592-019-0502-z}{\textbf{scMethylHiC\textsuperscript{\textbf{\large{+}}}}}\\\citealt{li2019}, no edge, fit=tight, name=scmethylhic, tier=2019]]
]]
]]
]]
[, empty, no edge[\href{https://www.nature.com/articles/cr201623}{\textbf{scTRIO-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{hou2016}, no edge, fit=tight, name=sctrio-seq, tier=2016
[, empty, no edge[\href{https://elifesciences.org/articles/23203}{\textbf{scNOMe-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{pott2017}, no edge, fit=tight, name=scnome-seq, tier=2017
[, empty, no edge[\href{https://science.sciencemag.org/content/361/6409/1380/tab-figures-data}{\textbf{sci-CAR\textsuperscript{\textbf{\large{+}}}}}\\\citealt{cao2018}, no edge, fit=tight, name=sci-car, tier=2018
[, empty, no edge[\href{https://www.nature.com/articles/s41467-018-08205-7}{\textbf{scCAT-seq\textsuperscript{\textbf{\large{+}}}}}\\\citealt{liu2019}, no edge, fit=tight, name=sccat-seq, tier=2019]]
]]
]]
]]
[, empty, no edge[\href{https://onlinelibrary.wiley.com/doi/full/10.1002/adbi.201900065}{\href{https://onlinelibrary.wiley.com/doi/full/10.1002/adbi.201900065}{\textbf{scRNA/ATAC-seq\textsuperscript{\textbf{\large{+}}}}}}\\\citealt{reyes2019}, no edge, fit=tight, name=reyes_scrna/atac-seq, tier=2019]]
]
% epigenomics
[, no edge, tier=2012
[, no edge, fit=band, tier=2019b, name=sep_epigenomics]
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.3035}{\textbf{scBS-seq}}\\\citealt{smallwood2014}, no edge, fit=band, name=scbs-seq, tier=2014
[\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847781/}{\textbf{scRRBS-seq}}\\\citealt{guo2015}, no edge, fit=band, name=scrrbs-seq, tier=2015]
]]
[, empty, no edge[\href{https://www.cell.com/cell-reports/fulltext/S2211-1247(15)00109-6}{\textbf{scWGBS}}\\\citealt{farlik2015}, no edge, fit=band, name=scwgbs, tier=2015]]
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.2688}{\textbf{ATAC-seq\textsuperscript{\large{*}}}}\\\citealt{buenrostro2013}, no edge, calign=child, calign child=3, fit=tight, name=atac-seq, tier=2013
[, empty, tier=2014b[\href{https://www.nature.com/articles/nmeth.4396}{\textbf{Omni-ATAC\textsuperscript{\large{*}}}}\\\citealt{corces2017}, fit=band, name=omni-atac, tier=2017
[, empty, edge=dotted[\href{https://www.nature.com/articles/s41467-018-07771-0}{\textbf{scATAC-seq}}\\\citealt{chen2018b}, edge=dotted, fit=tight, tier=2018]]
]]
[, empty, edge=dotted, tier=2014b[\href{https://science.sciencemag.org/content/348/6237/910}{\textbf{sciATAC-seq}}\\\citealt{cusanovich2015}, edge=dotted, fit=tight, name=sciatac-seq, tier=2015
[, empty, edge=dotted[\href{https://www.nature.com/articles/nbt.4038}{\textbf{scTHS-seq}}\\\citealt{lake2017b}, edge=dotted, fit=tight, name=scths-seq, tier=2017]]
[, empty, edge=dotted[\href{https://www.nature.com/articles/s41593-018-0079-3}{\textbf{snATAC-seq}}\\\citealt{preissl2018}, edge=dotted, fit=tight, name=scnatac-seq, tier=2018]]
[, empty, edge=dotted[\href{https://doi.org/10.1101/815720}{\textbf{sciMAP-ATAC\textsuperscript{\large{\textmu}}}}\\\citealt{thornton2019}, edge=dotted, fit=tight, name=scimap-atac, tier=2019]]
[, empty, edge=dotted[\href{https://doi.org/10.1038/nbt.4112}{\textbf{sci-MET}}\\\citealt{mulqueen2018}, edge=dotted, fit=tight, name=scnatac-seq, tier=2018]]
]]
[, empty, name=pre_dsciatac-seq, tier=2015b[\href{https://www.nature.com/articles/s41587-019-0147-6}{\textbf{dsciATAC-seq}}\\\citealt{lareau2019}, fit=tight, name=dsciatac-seq, tier=2019]]
[, no edge, empty, name=preicell8_scatac-seq, tier=2015[\href{https://www.nature.com/articles/nature14590}{\textbf{ICELL8 scATAC-seq}}\\\citealt{mezger2018}\\Takara Bio, no edge, fit=tight, name=icell8_scatac-seq, tier=2018]]
[, no edge, empty, name=prec1_scatac-seq[\href{https://www.nature.com/articles/nature14590}{\textbf{C1 scATAC-seq}}\\\citealt{buenrostro2015}\\Fluidigm, no edge, fit=tight, name=c1_scatac-seq, tier=2015
[, empty, name=pre_perturb-atac-seq[\href{https://www.nature.com/articles/nature14590}{\textbf{Perturb-ATAC}}\\\citealt{rubin2019}, fit=tight, name=perturb-atac, tier=2019]]
]]
[, no edge, empty, name=pre_10x_scatac-seq, tier=2015[\href{https://www.nature.com/articles/s41587-019-0206-z}{\textbf{scATAC-seq}}\\\citealt{satpathy2019}\\10x Genomics, no edge, fit=band, name=10x_scatac-seq, tier=2019]]
[, edge=dotted, empty, tier=2014b[\href{https://www.nature.com/articles/nmeth.4031}{\textbf{ATAC-see\textsuperscript{\large{\textmu}}}}\\\citealt{chen2016}, edge=dotted, fit=band, tier=2016]]
]]
[, empty, no edge, [\href{https://doi.org/10.1038/nprot.2015.127}{\textbf{scHi-C}}\\\citealt{nagano2015}, no edge, fit=band, tier=2015
[\href{https://doi.org/10.1038/nature21429}{\textbf{scHi-C}}\\\citealt{stevens2017}, edge=dotted, fit=band, tier=2017]
]]
[, empty, no edge, [\href{https://www.sciencedirect.com/science/article/pii/S0092867415010922}{\textbf{scDam-ID}}\\\citealt{kind2015}, no edge, fit=band, tier=2015]]
[, empty, no edge, [\href{https://www.nature.com/articles/nature15740}{\textbf{scDNAse-seq}}\\\citealt{jin2015}, no edge, fit=tight, tier=2015
[, empty, no edge, [\href{https://www.nature.com/articles/s41556-019-0383-5}{\textbf{sc-itChIP-seq}}\\\citealt{ai2019}, no edge, fit=band, tier=2019]]
]]
[, cempty, no edge, [\href{https://www.nature.com/articles/nbt.3383}{\textbf{Drop-ChIP}}\\\citealt{rotem2015}, no edge, fit=band, tier=2015
[, empty, no edge, [\href{https://doi.org/10.1038/s41588-019-0424-9}{\textbf{scChIP-seq}}\\\citealt{grosselin2019}, no edge, fit=band, tier=2019]]
]]
]
% genomics
[, no edge, fit=band, tier=2019b, name=sep_genomics]
[, no edge, calign=center, tier=base
[, empty, no edge[\href{https://science.sciencemag.org/content/356/6334/189}{\textbf{LIANTI}}\\\citealt{chen2017}, no edge, fit=band, name=LIANTI, tier=2017]]
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.4140}{\textbf{DLP}}\\\citealt{zahn2017}, no edge, fit=band, tier=2017]]
[, empty, no edge[\href{https://www.nature.com/articles/nbt.3880}{\textbf{SiC-seq}}\\\citealt{lan2017}, no edge, fit=band, tier=2017]]
[, empty, no edge[\href{https://www.nature.com/articles/nmeth.4154}{\textbf{SCI-seq}}\\\citealt{vitak2017}, no edge, fit=band, name=sci-seq, tier=2017]]
]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[, no edge, fit=band, tier=2019b, name=sep_final]
[, empty, no edge, tier=base[, empty, no edge
[\textbf{\large{1992}}, no edge, name=1992r, tier=1992[, empty, no edge, tier=1992b
[\textbf{\large{2006}}, no edge, name=2006r, tier=2006[, empty, no edge, tier=2006b
[\textbf{\large{2007}}, no edge, tier=2007[, empty, no edge, tier=2007b
[\textbf{\large{2008}}, no edge, tier=2008[, empty, no edge, tier=2008b
[\textbf{\large{2009}}, no edge, tier=2009[, empty, no edge, tier=2009b
[\textbf{\large{2010}}, no edge, tier=2010[, empty, no edge, tier=2010b
[\textbf{\large{2011}}, no edge, tier=2011[, empty, no edge, tier=2011b
[\textbf{\large{2012}}, no edge, tier=2012[, empty, no edge, tier=2012b
[\textbf{\large{2013}}, no edge, tier=2013[, empty, no edge, tier=2013b
[\textbf{\large{2014}}, no edge, tier=2014[, empty, no edge, tier=2014b
[\textbf{\large{2015}}, no edge, tier=2015[, empty, no edge, tier=2015b
[\textbf{\large{2016}}, no edge, tier=2016[, empty, no edge, tier=2016b
[\textbf{\large{2017}}, no edge, tier=2017[, empty, no edge, tier=2017b
[\textbf{\large{2018}}, no edge, tier=2018[, empty, no edge, tier=2018b
[\textbf{\large{2019}}, no edge, tier=2019[, empty, no edge, tier=2019b
]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]
]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\draw (19, -1) rectangle (29, -9);
\node[right] at (20, -2) {\Large\textbf{Legend}};
\draw[] (20, -3) -- node[right=2.5cm] {\large Direct continuation} (23, -3);
\draw[dotted] (20, -4) -- node[right=2.5cm] {\large Inspired} (23, -4);
\draw[squiggly] (20, -5) -- node[right=2.5cm] {\large Commercial} (23, -5);
\node at (21.5, -6) {\large\textbf{*}} (23, -6);
\node[right] at (24, -6) {\large Bulk method};
\node at (21.5, -7) {\large\textbf{\textmu}} (23, -7);
\node[right] at (24, -7) {\large Spatial/imaging};
\node at (21.5, -8) {\large\textbf{+}} (23, -8);
\node[right] at (24, -8) {\large Multiomic method};
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\draw[decoration={brace, amplitude=20pt, raise=38cm}, decorate, ultra thick] (sep_proteomics) -- node[above=39cm] {\Huge \textbf{Single Cell Technology}} ($(sep_final)+(-1cm, 0)$);
\draw[decoration={brace, amplitude=20pt, raise=8cm}, decorate, ultra thick] ($(sep_proteomics)+(-0.5cm, 0)$) ++ (1cm, 0) -- node[above=9cm] {\Huge \textbf{Proteomics}} (sep_transcriptomics);
\draw[decoration={brace, amplitude=20pt, raise=35cm}, decorate, ultra thick] (sep_transcriptomics) -- node[above=36cm] {\Huge \textbf{Transcriptomics}} (sep_multiomics);
\draw[decoration={brace, amplitude=20pt, raise=15cm}, decorate, ultra thick] (sep_transcriptomics) -- node[above=16cm] {\Huge \textbf{Spatial Transcriptomics}} (sep_spatial_transcriptomics);
\draw[decoration={brace, amplitude=20pt, raise=12cm}, decorate, ultra thick] (sep_multiomics) -- node[above=13cm] {\Huge \textbf{Multiomics}} (sep_epigenomics);
\draw[decoration={brace, amplitude=20pt, raise=17cm}, decorate, ultra thick] (sep_epigenomics) -- node[above=18cm] {\Huge \textbf{Epigenomics}} (sep_genomics);
\draw[decoration={brace, amplitude=20pt, raise=8cm}, decorate, ultra thick] (sep_genomics) -- node[above=9cm] {\Huge \textbf{Genomics}} ($(sep_final)+(-0cm, 0)$);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\draw[dotted, ultra thick] (1992r.south) -- (2006r.north);
\draw[dotted, ultra thick] (1992l.south) -- (2006l.north);
\draw[squiggly] (smart-seq22.210) to[out=220, in=350] (chromium2016);
\draw[squiggly] (smart-seq) -- (c1_scrna-seq);
\draw[squiggly] (smart-seq2) -- (c1_scrna-seq2);
\draw[squiggly] (c1_scrna-seq) -- (c1_scrna-seq2);
\draw[squiggly] (strt-seq2012) -- (c1-strt-seq);
\draw[squiggly] (atac-seq) -- (c1_scatac-seq);
\draw[squiggly] (atac-seq) -- (preicell8_scatac-seq);
\draw[squiggly] (preicell8_scatac-seq) -- (icell8_scatac-seq);
\draw[squiggly] (atac-seq) -- (pre_10x_scatac-seq);
\draw[squiggly] (pre_10x_scatac-seq) -- (10x_scatac-seq);
\draw[dotted, thick] (rna-seq) -- (mrna-seq);
\draw[dotted, thick] (chromium2016) -- (perturb-seq);
\draw[dotted, thick] (drop-seq) -- (presnare-seq);
\draw[dotted, thick] (drop-seq) -- (dronc-seq);
\draw[dotted, thick] (strt-seq.south) -- (smart-seq.north);
\draw[dotted, thick] (smart-seq22) to[out=10, in=168] (sccat-seq);
\draw[dotted, thick] (smart-seq22) to[out=357, in=160] (reyes_scrna/atac-seq);
\draw[dotted, thick] (smart-seq22) to[out=5, in=170] (gt-seq);
\draw[dotted, thick] (omni-atac) -- (sccat-seq);
\draw[dotted, thick] (omni-atac) -- (reyes_scrna/atac-seq);
\draw[dotted, thick] (scbs-seq) -- (scmt-seq);
\draw[dotted, thick] (gt-seq) -- (scmt-seq);
\draw[dotted, thick] (gt-seq) -- (sctrio-seq);
\draw[dotted, thick] (scnome-seq) -- (scnmt-seq);
\draw[dotted, thick] (scrrbs-seq) -- (sctrio-seq);
\draw[dotted, thick] (sciatac-seq) -- (pre_dsciatac-seq);
\draw[] (scirna-seq) to[out=330, in=140] (sci-car);
\draw[] (scirna-seq) -- (sci-l3);
\draw[] (sciatac-seq) -- (sci-car);
% \draw[] (sciatac-seq) to[out=210, in=0] (scirna-seq);
\end{forest}
\end{center}
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\clearpage
\bibliographystyle{humannat}
\bibliography{scforest_bibliography.bib}
\end{document}