From bca90222f3bd1f9345bab7e95842425a2649a766 Mon Sep 17 00:00:00 2001 From: ndwarshuis Date: Fri, 30 Jul 2021 17:44:17 -0400 Subject: [PATCH] ADD experimental overview and fold change/viability plots to il15 data --- figures/il15_blockade_1.svg | 2303 ++++++++++++++++++++++++++++++++++- figures/il15_blockade_2.svg | 1764 ++++++++++++++++++++++++++- tex/thesis.tex | 24 +- 3 files changed, 3990 insertions(+), 101 deletions(-) diff --git a/figures/il15_blockade_1.svg b/figures/il15_blockade_1.svg index 2d3628a..10d9a5a 100644 --- a/figures/il15_blockade_1.svg +++ b/figures/il15_blockade_1.svg @@ -445,6 +445,538 @@ d="m 213.29,204.14 h 74.37 v 17.15 h -74.37 z" id="path33588" /> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bead + + + + + + + + + + + + + + + + DMS + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 5 + 10 + + + + + + + + + + + + + + + + + + 0 + 5 + 10 + + + + + + + + + + + + + + 0% + 25% + 50% + 75% + 100% + + + + + + + + + + + + + + + + + + + + Time (days) + + + + Viability + + + + + + + + + + + + + + + + IL15Ra Block + + + + + + + + + + + + + + + + + + + + + + + + + + + FALSE + + + + + + + TRUE + + + + + + + + + + + + + + + + transform="matrix(1.3333333,0,0,-1.3333333,7.066683,620.18669)"> - - fold change - viability - a. + x="0.72211659" + y="136">b. a. + b. + x="286.00003" + y="136">c. c. + x="1.2924291" + y="318.00003">d. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bead + + + + + + + + + + + + + + + + DMS + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 5 + 10 + + + + + + + + + + + + + + + + + + 0 + 5 + 10 + + + + + + + + + + + + + + 0.0e+00 + 5.0e+06 + 1.0e+07 + 1.5e+07 + 2.0e+07 + + + + + + + + + + + + + + + + + + + + Time (days) + + + + Number of cells + + + + + + + + + + + + + + + + IL15Ra Block + + + + + + + + + + + + + + + + + + + + + + + + + + + FALSE + + + + + + + TRUE + + + + + + + + + + + + + + + + + + + + + + + + + + + D0 + D6 + D4 + D2 + D14 + Activate + Harvest + + + + Add anti-IL15Ror isotype control(5mg/ml) diff --git a/figures/il15_blockade_2.svg b/figures/il15_blockade_2.svg index a46bdb3..2eddf8f 100644 --- a/figures/il15_blockade_2.svg +++ b/figures/il15_blockade_2.svg @@ -298,6 +298,104 @@ d="m 212.85,205.02 h 74.81 v 16.27 h -74.81 z" id="path44124" /> + + + + + + + + + + + + + + + + + + + + + + + + + + + + transform="matrix(1.3333333,0,0,-1.3333333,9.293345,592.96002)"> - - a. + x="0.26512516" + y="125.30667">b. a. + b. + x="210.61337" + y="125.30667">c. c. + x="0.83543766" + y="292">d. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0e+00 + 2e+08 + 4e+08 + 6e+08 + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 5 + 10 + + + + + + + + Time (days) + + + + Number of cells + + + + + + + + + + + + + + + + IL15 Block + + + + + + + + + + + + + + + + + + + + + + + + + + + FALSE + + + + + + + TRUE + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0% + 25% + 50% + 75% + 100% + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 5 + 10 + + + + + + + + Time (days) + + + + Viability + + + + + + + + + + + + + + + + IL15 Block + + + + + + + + + + + + + + + + + + + + + + + + + + + FALSE + + + + + + + TRUE + + + + + + + + + + + + + + + + + + + + + + + + + + fold change + id="tspan111335" + x="30.248056" + y="32.02758">D0 viability + id="tspan111335-2" + x="102.23439" + y="32.02758">D6 + D8 + D4 + D2 + D14 + Activate + Harvest + + + + + Add anti-IL15or isotype control(5mg/ml) diff --git a/tex/thesis.tex b/tex/thesis.tex index 85a8294..a581bbd 100644 --- a/tex/thesis.tex +++ b/tex/thesis.tex @@ -3033,27 +3033,31 @@ many conditions, we hypothesized that \gls{il15} may be responsible for this, and further that the unique \textit{cis/trans} activity of \gls{il15} may be more active in the \gls{dms} system due to higher cell density. -% 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_overview} \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. + {Blocking IL15Ra does not lead to differences in memory or growth. + \subcap{fig:il15_1_overview}{Experimental overview} + Longitudinal measurements of + \subcap{fig:il15_1_fc}{fold change} and + \subcap{fig:il15_1_viability}{viability} for blocked and unblocked + conditions expanded with either beads or \glspl{dms}. + \subcap{fig:il15_1_mem}{Flow cytometry markers for \gls{dms}-expanded T + cells at day 14 for blocked and unblocked groups.}. } \label{fig:il15_1} \end{figure*} % TODO how did I determine how much to add? -% TODO how often was this added? % TODO just gate these as normal because this looks sketchy We first tested this hypothesis by blocking \gls{il15r} with either a specific \gls{mab} or an \gls{igg} isotype control. We observed no difference in the @@ -3070,13 +3074,21 @@ the markers, and by extension showing no difference in phenotype \begingroup \includegraphics{../figures/il15_blockade_2.png} + \phantomsubcaption\label{fig:il15_2_overview} \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. + {Blocking soluble IL15 does not lead to differences in memory or growth. + \subcap{fig:il15_2_overview}{Experimental overview} + Longitudinal measurements of + \subcap{fig:il15_2_fc}{fold change} and + \subcap{fig:il15_2_viability}{viability} for blocked and unblocked + conditions expanded with \glspl{dms}. + \subcap{fig:il15_2_mem}{Flow cytometry markers for \gls{dms}-expanded T + cells at day 14 for blocked and unblocked groups.}. } \label{fig:il15_2} \end{figure*}