ADD figures to aim 2b

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Nathan Dwarshuis 2021-07-26 18:16:21 -04:00
parent 197aee093f
commit 758b04c967
8 changed files with 18709 additions and 1 deletions

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@ -85,6 +85,9 @@
\newacronym{a2b2}{A2B2}{integrin $\upalpha$1$\upbeta$2} \newacronym{a2b2}{A2B2}{integrin $\upalpha$1$\upbeta$2}
\newacronym{til}{TIL}{tumor infiltrating lymphocytes} \newacronym{til}{TIL}{tumor infiltrating lymphocytes}
\newacronym{nsg}{NSG}{NOD scid gamma} \newacronym{nsg}{NSG}{NOD scid gamma}
\newacronym{colb}{COL-B}{collagenase B}
\newacronym{cold}{COL-D}{collagenase D}
\newacronym{tsne}{tSNE}{t-stochastic neighbor embedding}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SI units for uber nerds % SI units for uber nerds
@ -1063,6 +1066,8 @@ cells after \SI{14}{\day} were on the interior surface of the \glspl{dms}
%, and this did not significantly change with initial seeding density (Supplemental Table 1). %, and this did not significantly change with initial seeding density (Supplemental Table 1).
% FIGURE caspase/bcl2 figure
% TODO add this to the methods section % TODO add this to the methods section
% TODO double check the timing of this experiment (it might not be day 14) % TODO double check the timing of this experiment (it might not be day 14)
% TODO provide the regression results and coefficients from this % TODO provide the regression results and coefficients from this
@ -1553,6 +1558,7 @@ provide these benefits.
\subsection{DOE shows optimal conditions for expanded potent T cells} \subsection{DOE shows optimal conditions for expanded potent T cells}
% FIGURE IL2 modulation figure
% TODO not all of these were actually use, explain why by either adding columns % TODO not all of these were actually use, explain why by either adding columns
% or marking with an asterisk % or marking with an asterisk
@ -1642,6 +1648,142 @@ provide these benefits.
\section{introduction} \section{introduction}
\section{methods} \section{methods}
\section{results} \section{results}
\subsection{adding or removing DMSs alters expansion and phenotype}
% TODO this figure is tall and skinny like me
\begin{figure*}[ht!]
\begingroup
\includegraphics{../figures/collagenase.png}
\endgroup
\caption[Effects Collagenase Treatment on T cells]
{T cells treated with either \gls{colb}, \gls{cold}, or buffer and then
stained for various surface markers and analyzing via flow cytometry.}
\label{fig:collagenase_fx}
\end{figure*}
% TODO this figure still says "carrier"
\begin{figure*}[ht!]
\begingroup
\includegraphics{../figures/add_remove_endpoint.png}
\phantomsubcaption\label{fig:add_rem_growth}
\phantomsubcaption\label{fig:add_rem_viability}
\phantomsubcaption\label{fig:add_rem_cd4}
\endgroup
\caption[Endpoint results from adding/removing \gls{dms} on day 4]
{Changing \gls{dms} concentration on day 4 has profound effects on phenotype
and growth.
\subcap{fig:add_rem_growth}{Longitudinal fold change},
\subcap{fig:add_rem_viability}{longitudinal viability}, and
\subcap{fig:add_rem_cd4}{day 14 \pthp{}} of T cell cultures with \glspl{dms}
added, removed, or kept the same on day 4.
}
\label{fig:add_rem}
\end{figure*}
% TODO this needs some better annotations
\begin{figure*}[ht!]
\begingroup
\includegraphics{../figures/add_remove_spade.png}
\phantomsubcaption\label{fig:spade_msts}
\phantomsubcaption\label{fig:spade_tsne_all}
\phantomsubcaption\label{fig:spade_tsne_stem}
\phantomsubcaption\label{fig:spade_quant}
\endgroup
\caption[SPADE and tSNE analysis temporally-modified DMS concentration]
{Removing \glspl{dms} leads to a higher fraction of potent stem-memory T
cells compared to both adding and not changing the \gls{dms} concentration
at day 4.
\subcap{fig:spade_msts}{SPADE plots of CD4, CD45RA, CD27, and CD45RO
expression on T cells. All cells from the added, removed, or no change
groups were pooled and clustered at once.}
\subcap{fig:spade_tsne_all}{\gls{tsne} plots of all cells pooled from all
groups.}
\subcap{fig:spade_tsne_stem}{\gls{tsne} plots of T cells from all groups
manually gated on \cdp{8}\cdp{27}\cdp{45RO}.}
\subcap{fig:spade_quant}{T cells from SPADE plots clustered by expression in
(\subref{fig:spade_msts}) quantified against total cell number from each
group.}
}
\label{fig:spade}
\end{figure*}
\subsection{blocking integrin binding does not alter expansion or phenotype}
% TODO perhaps these figs should be combined
% TODO actually make the captions for these
% TODO add some background into why integrins are important and the proposed mechanism
\begin{figure*}[ht!]
\begingroup
\includegraphics{../figures/integrin_1.png}
\phantomsubcaption\label{fig:inegrin_1_fc}
\phantomsubcaption\label{fig:inegrin_1_mem}
\phantomsubcaption\label{fig:inegrin_1_cd49}
\endgroup
\caption[Integrin blocking I]
{Blocking with integrin does not lead to differences in memory or growth.
}
\label{fig:integrin_1}
\end{figure*}
\begin{figure*}[ht!]
\begingroup
\includegraphics{../figures/integrin_2.png}
\phantomsubcaption\label{fig:inegrin_2_fc}
\phantomsubcaption\label{fig:inegrin_2_mem}
\endgroup
\caption[Integrin blocking II]
{Blocking with integrin does not lead to differences in memory or growth.
}
\label{fig:integrin_2}
\end{figure*}
\subsection{blocking IL15 signaling does not alter expansion or phenotype}
% TODO actually add captions
% TODO add fold change and viability to these
% TODO maybe combine these
% TODO add some background into why IL15 is important and the proposed mechanism
\begin{figure*}[ht!]
\begingroup
\includegraphics{../figures/il15_blockade_1.png}
\phantomsubcaption\label{fig:il15_1_fc}
\phantomsubcaption\label{fig:il15_1_viability}
\phantomsubcaption\label{fig:il15_1_mem}
\endgroup
\caption[IL15 blocking I]
{Blocking with IL15 does not lead to differences in memory or growth.
}
\label{fig:il15_1}
\end{figure*}
\begin{figure*}[ht!]
\begingroup
\includegraphics{../figures/il15_blockade_2.png}
\phantomsubcaption\label{fig:il15_2_fc}
\phantomsubcaption\label{fig:il15_2_viability}
\phantomsubcaption\label{fig:il15_2_mem}
\endgroup
\caption[IL15 blocking II]
{Blocking with IL15 does not lead to differences in memory or growth.
}
\label{fig:il15_2}
\end{figure*}
\section{discussion} \section{discussion}
\chapter{aim 3}\label{aim3} \chapter{aim 3}\label{aim3}