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% Document Info
\author{scarlettnicole87}
\pdfinfo{
  /Title (assay-design.pdf)
  /Creator (Cheatography)
  /Author (scarlettnicole87)
  /Subject (Assay Design Cheat Sheet)
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\noindent
\begin{multicols}{3}
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    \vspace{-7pt}
    {\parbox{\dimexpr\textwidth-2\fboxsep\relax}{\noindent
        \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}}
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\begin{tabulary}{11cm}{L}
    \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{Assay Design Cheat Sheet}}}} \\
    \normalsize{by \textcolor{DarkBackground}{scarlettnicole87} via \textcolor{DarkBackground}{\uline{cheatography.com/147014/cs/31908/}}}
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  \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}}  \\
  \vspace{-2pt}scarlettnicole87 \\
  \uline{cheatography.com/scarlettnicole87} \\
  \end{tabulary}
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  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}}  \\
   \vspace{-2pt}Not Yet Published.\\
   Updated 28th April, 2022.\\
   Page {\thepage} of \pageref{LastPage}.
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  %\includegraphics[width=48px,height=48px]{dave.jpeg}
  Measure your website readability!\\
  www.readability-score.com
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\begin{document}
\raggedright
\raggedcolumns

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\footnotesize % Small font.

\begin{multicols*}{3}

\begin{tabularx}{5.377cm}{x{1.69218 cm} x{3.28482 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Transgenes (TG)}}  \tn
% Row 0
\SetRowColor{LightBackground}
Basic Vector TG & Can target anywhere \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
TG with some homology & Target to least homologous region \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
\seqsplit{Promoter-Vector} TG & Target at promoter-vector junction \tn 
% Row Count 6 (+ 2)
% Row 3
\SetRowColor{white}
Mouse cDNA & Target at exon-exon junction (Be aware of intron size) \tn 
% Row Count 9 (+ 3)
% Row 4
\SetRowColor{LightBackground}
Human TG & Target to least homologous region \tn 
% Row Count 11 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.09034 cm} x{2.88666 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{SNPs (MUT)}}  \tn
% Row 0
\SetRowColor{LightBackground}
Basic SNP & Center SNPs in reporter oligos. \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
SNP based off AA change given & Locate AA change. Center SNPs in reporter oligos. \tn 
% Row Count 5 (+ 3)
% Row 2
\SetRowColor{LightBackground}
rs\# & Locate rs\#. Ensure reporter 1 is BL6 sequence. Center SNPs in reporter oligos. \tn 
% Row Count 9 (+ 4)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{{\bf{Both reporters MUST be on the same strand or the assay will not work.}}}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.18988 cm} x{2.78712 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Humanized Models (KO)}}  \tn
% Row 0
\SetRowColor{LightBackground}
Standard humanized KO model & Identify endogenous human junction and include 2-3 mismatches per oligo (WT and Mutant) if possible. \tn 
% Row Count 5 (+ 5)
% Row 1
\SetRowColor{white}
Humanized model with FRT or LoxP & Target flanking the FRT/LoxP which allows you to avoid homology \tn 
% Row Count 8 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.84149 cm} x{3.13551 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Knockouts (KO)}}  \tn
% Row 0
\SetRowColor{LightBackground}
Standard KO Model & Target KO assay at 5' or 3' junction \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
Small CRISPR deletion & Balance KO probe across new junction \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
Large CRISPR deletion & Flank new junction \tn 
% Row Count 6 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{{\bf{Designs for corresponding WT will be noted in the wildtype section.}}}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.44333 cm} x{3.53367 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{KO landmarks}}  \tn
% Row 0
\SetRowColor{LightBackground}
Start/Stop & Design WT at start or stop (depending on model). KO probe will be a generic. \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
Coding Region & Design anywhere in coding region. KO probe will be a generic \tn 
% Row Count 6 (+ 3)
% Row 2
\SetRowColor{LightBackground}
\seqsplit{Restriction} Site & Design according to restriction sites. KO probe will be a generic. \tn 
% Row Count 9 (+ 3)
% Row 3
\SetRowColor{white}
\seqsplit{Coordinates} & Design according to coordinates. KO probe will be a generic. \tn 
% Row Count 12 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{{\bf{When in doubt - SEQUENCE.}}}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.4885 cm} x{2.4885 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Wildtypes (WT)}}  \tn
% Row 0
\SetRowColor{LightBackground}
WT for small insertion (\textless{}400bp) & Balance probe (40/30) or do allele specific primer. \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
WT for large insertion (\textgreater{}400bp) & Can flank insertion site or have a probe across insertion site but do NOT need to balance. \tn 
% Row Count 8 (+ 5)
% Row 2
\SetRowColor{LightBackground}
WT where some bases were deleted (either via CRISPR or upon insertion of vector) & Target probe within deleted bases. Primers can be on either side. \tn 
% Row Count 12 (+ 4)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{2.33919 cm} x{2.63781 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Floxed (FL or MD)}}  \tn
% Row 0
\SetRowColor{LightBackground}
Floxed allele with vector & Flank LoxP, use tearpin, or break the hairpin. \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
Floxed allele with minimal vector & Use tearpin or break the hairpin \tn 
% Row Count 5 (+ 2)
% Row 2
\SetRowColor{LightBackground}
Floxed allele when unsure which LoxP & Flank LoxP or do tearpin \tn 
% Row Count 7 (+ 2)
% Row 3
\SetRowColor{white}
Marker deleted floxed allele & Flank FRT/LoxP \tn 
% Row Count 9 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{{\bf{Identify which LoxP you have. If you are breaking the hairpin you MUST know which LoxP to ensure you break in the correct direction.}}}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{x{1.74195 cm} x{3.23505 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Excised (EX)}}  \tn
% Row 0
\SetRowColor{LightBackground}
EX with vector & Flank remaining LoxP or tearpin. \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
EX with minimal vector & Tearpin or can flank LoxP if large enough deletion created by Cre recombination. \tn 
% Row Count 6 (+ 4)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{5.377cm}{p{0.4977 cm} x{4.4793 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{CRISPR}}  \tn
% Row 0
\SetRowColor{LightBackground}
NHEJ & Flank new junction created as long as it is \textgreater{}400bp \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
HDR & Must target 1 oligo outside of ssODN to be site specific. \tn 
% Row Count 4 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{{\bf{Remember that CRISPR rules can apply to a variety of models including SNPs, Conditional lines, and even traditional KOs. Please be aware if you are designing for CRISPR and utilize our best practices.}}}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}


% That's all folks
\end{multicols*}

\end{document}