ADD figures to aim 2b

tex/thesis.tex

@@ -85,6 +85,9 @@
 \newacronym{a2b2}{A2B2}{integrin $\upalpha$1$\upbeta$2}
 \newacronym{til}{TIL}{tumor infiltrating lymphocytes}
 \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
@@ -718,7 +721,7 @@ entailed adding sterile \gls{pbs} in a 10:1 volumetric ratio, agitating at
 reaction volume.
 
 To coat with \gls{stp}, \SI{40}{\ug\per\mL} \product{\gls{stp}}{Jackson
-  Immunoresearch}{ 016-000-114} was added and allowed to react for
+  Immunoresearch}{016-000-114} was added and allowed to react for
 \SI{60}{\minute} at \SI{700}{RPM} of agitation. After the reaction, supernatant
 was taken for the \gls{bca} assay, and the carriers were washed analogously to
 the previous wash step to remove the biotin, except two washes were done and the
@@ -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).
 
+% FIGURE caspase/bcl2 figure
+
 % TODO add this to the methods section
 % TODO double check the timing of this experiment (it might not be day 14)
 % 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}
 
+% FIGURE IL2 modulation figure
 
 % TODO not all of these were actually use, explain why by either adding columns
 % or marking with an asterisk
@@ -1642,6 +1648,142 @@ provide these benefits.
 \section{introduction}
 \section{methods}
 \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}
 
 \chapter{aim 3}\label{aim3}