ADD methods for apoptotic marker quantification

This commit is contained in:
Nathan Dwarshuis 2021-07-27 12:19:06 -04:00
parent b0e0f420eb
commit afbb5fadbd
1 changed files with 56 additions and 14 deletions

View File

@ -88,8 +88,12 @@
\newacronym{colb}{COL-B}{collagenase B} \newacronym{colb}{COL-B}{collagenase B}
\newacronym{cold}{COL-D}{collagenase D} \newacronym{cold}{COL-D}{collagenase D}
\newacronym{tsne}{tSNE}{t-stochastic neighbor embedding} \newacronym{tsne}{tSNE}{t-stochastic neighbor embedding}
\newacronym{anv}{ANX-V}{Annexin-V} \newacronym{anv}{AXV}{Annexin-V}
\newacronym{pi}{PI}{propidium iodide} \newacronym{pi}{PI}{propidium iodide}
\newacronym{rt}{RT}{room temperature}
\newacronym{cas37}{Cas3/7}{Caspase-3/7}
\newacronym{bcl2}{BCL-2}{B cell lymphoma 2}
\newacronym{tmb}{TMB}{3,3',5,5'-Tetramethylbenzidine}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SI units for uber nerds % SI units for uber nerds
@ -103,7 +107,10 @@
\DeclareSIUnit\dms{DMS} \DeclareSIUnit\dms{DMS}
\DeclareSIUnit\cell{cells} \DeclareSIUnit\cell{cells}
\DeclareSIUnit\ab{mAb} \DeclareSIUnit\ab{mAb}
\DeclareSIUnit\normal{N}
\DeclareSIUnit\molar{M} \DeclareSIUnit\molar{M}
\DeclareSIUnit\mM{\milli\molar}
\DeclareSIUnit\uM{\micro\molar}
\DeclareSIUnit\gforce{\times{} g} \DeclareSIUnit\gforce{\times{} g}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@ -710,7 +717,7 @@ carried out at \SI{20}{\mg\per\ml} carriers at room temperature and agitated
using an orbital shaker with a \SI{3}{\mm} orbit diameter. After autoclaving, using an orbital shaker with a \SI{3}{\mm} orbit diameter. After autoclaving,
the microcarriers were washed using sterile \gls{pbs} three times in a 10:1 the microcarriers were washed using sterile \gls{pbs} three times in a 10:1
volume ratio. \product{\Gls{snb}}{\thermo}{21217} was dissolved at volume ratio. \product{\Gls{snb}}{\thermo}{21217} was dissolved at
approximately \SI{10}{\micro\molar} in sterile ultrapure water, and the true approximately \SI{10}{\uM} in sterile ultrapure water, and the true
concentration was then determined using the \gls{haba} assay (see below). concentration was then determined using the \gls{haba} assay (see below).
\SI{5}{\ul\of{\ab}\per\mL} \gls{pbs} was added to carrier suspension and allowed \SI{5}{\ul\of{\ab}\per\mL} \gls{pbs} was added to carrier suspension and allowed
to react for \SI{60}{\minute} at \SI{700}{\rpm} of agitation. After the to react for \SI{60}{\minute} at \SI{700}{\rpm} of agitation. After the
@ -725,16 +732,17 @@ reaction volume.
To coat with \gls{stp}, \SI{40}{\ug\per\mL} \product{\gls{stp}}{Jackson 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 \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 was taken for the \product{\gls{bca} assay}{\thermo}{23225}, and the carriers
the previous wash step to remove the biotin, except two washes were done and the were washed analogously to the previous wash step to remove the biotin, except
agitation time was \SI{30}{\minute}. Biotinylated \glspl{mab} against human CD3 two washes were done and the agitation time was \SI{30}{\minute}. Biotinylated
\catnum{\bl}{317320} and CD28 \catnum{\bl}{302904} were combined in a 1:1 mass \glspl{mab} against human CD3 \catnum{\bl}{317320} and CD28 \catnum{\bl}{302904}
ratio and added to the carriers at \SI{0.2}{\ug\of{\ab}\per\mg\of{\dms}}. Along were combined in a 1:1 mass ratio and added to the carriers at
with the \glspl{mab}, sterile \product{\gls{bsa}}{Sigma}{A9576} was added to a \SI{0.2}{\ug\of{\ab}\per\mg\of{\dms}}. Along with the \glspl{mab}, sterile
final concentration of \SI{2}{\percent} in order to prevent non-specific binding \product{\gls{bsa}}{Sigma}{A9576} was added to a final concentration of
of the antibodies to the reaction tubes. \glspl{mab} were allowed to bind to the \SI{2}{\percent} in order to prevent non-specific binding of the antibodies to
carriers for \SI{60}{\minute} with \SI{700}{\rpm} agitation. After binding, the reaction tubes. \glspl{mab} were allowed to bind to the carriers for
supernatants were sampled to quantify remaining \gls{mab} concentration using an \SI{60}{\minute} with \SI{700}{\rpm} agitation. After binding, supernatants were
sampled to quantify remaining \gls{mab} concentration using an
\product{\anti{\gls{igg}} \gls{elisa} kit}{Abcam}{157719}. Fully functionalized \product{\anti{\gls{igg}} \gls{elisa} kit}{Abcam}{157719}. Fully functionalized
\glspl{dms} were washed in sterile \gls{pbs} analogous to the previous washing \glspl{dms} were washed in sterile \gls{pbs} analogous to the previous washing
step to remove excess \gls{stp}. They were washed once again in the cell culture step to remove excess \gls{stp}. They were washed once again in the cell culture
@ -767,7 +775,7 @@ extinction coefficient at \SI{500}{\nm} for \gls{haba}/avidin was assumed to be
\SI{34000}{\per\cm\per\molar}. \SI{34000}{\per\cm\per\molar}.
\gls{stp} binding to the carriers was quantified indirectly using a \gls{stp} binding to the carriers was quantified indirectly using a
\product{\gls{bca} kit }{\thermo}{23227} according to the manufacturers \product{\gls{bca} kit}{\thermo}{23227} according to the manufacturers
instructions, with the exception that the standard curve was made with known instructions, with the exception that the standard curve was made with known
concentrations of purified \gls{stp} instead of \gls{bsa}. Absorbance at concentrations of purified \gls{stp} instead of \gls{bsa}. Absorbance at
\SI{592}{\nm} was quantified using a Biotek plate reader. \SI{592}{\nm} was quantified using a Biotek plate reader.
@ -826,6 +834,40 @@ Cells on the \glspl{dms} were visualized by adding \SI{0.5}{\ul}
\product{\acd{45}-\gls{af647}}{\bl}{368538}, incubating for \SI{1}{\hour}, and \product{\acd{45}-\gls{af647}}{\bl}{368538}, incubating for \SI{1}{\hour}, and
imaging on a spinning disk confocal microscope. imaging on a spinning disk confocal microscope.
\subsection{quantification of apoptosis using Annexin-V}
Apoptosis was quantified using \gls{anv} according to the manufacturer's
instructions. Briefly, cells were transferred to flow tubes and washed twice
with \gls{pbs} by adding \SI{3}{\ml} to each tube, centrifuging for
\SI{400}{\gforce}, and aspirating the liquid down to \SI{200}{\ul}. The cells
were analogously washed a third time with staining buffer (\SI{10}{\mM} HEPES,
\SI{140}{\mM} NaCl, \SI{2.5}{\mM} CaCl\textsubscript{2}) and aspirated down to a
final volume of \SI{100}{\ul}. Cells were stained in this volume with
\SI{1}{\ul} \product{\gls{anv}-\gls{fitc}}{\bl}{640906} and \SI{5}{\ul}
\product{\gls{pi}}{\thermo}{P3566} and incubated for \SI{15}{\minute} at gls{rt}
in the dark. After incubation, \SI{400}{\ul} staining buffer was added to each
tube. Each tube was then analyzed via flow cytometry.
\subsection{quantification of Caspase-3/7}
\Gls{cas37} was quantified using \product{CellEvent dye}{\thermo}{C10723}
according the manufacturer's instructions. Briefly, a 2X (\SI{8}{\mM}) working
solution of CellEvent dye was added to \SI{100}{\ul} cell suspension (at least
\num{5e4} cells) and incubated at \SI{37}{\degreeCelsius} for \SI{30}{\minute}.
After incubation, cells were immediately analyzed via flow cytometry.
\subsection{quantification of BCL-2}
\Gls{bcl2} was quantified using an \product{Human Total Bcl-2 DuoSet \gls{elisa}
kit}{Rnd Systems}{DYC827B-2} according to the manufacturer's instructions and
supplemented with \product{5X diluent buffer}{\bl}{421203}, \product{\gls{tmb}
substrate solution}{eBioscience}{00-4201-56}, and \SI{2}{\normal}
H\textsubscript{2}SO\textsubscript{4} stop solution made in house. Briefly,
cells were lysed using \product{10X lysis buffer}{Cell Signaling}{9803S}, and
the lysate was quantified for protein using a \product{\gls{bca}
assay}{\thermo}{23225} as directed. Standardized lysates were measured using
the \gls{elisa} kit as directed.
\subsection{chemotaxis assay} \subsection{chemotaxis assay}
% TODO not sure about the transwell product number % TODO not sure about the transwell product number
@ -882,7 +924,7 @@ plates and incubated for another \SI{24}{\hour}. Cells and beads/\glspl{dms}
were removed from the retronectin plates using vigorous pipetting and were removed from the retronectin plates using vigorous pipetting and
transferred to another 96 well plate wherein expansion continued. transferred to another 96 well plate wherein expansion continued.
% METHOD for apoptosis quantification
\subsection{statistical analysis} \subsection{statistical analysis}