Data from: ZBP1 mediated restriction of Toxoplasma gondii in both the early acute and chronic brain stages of infection
Data files
May 18, 2026 version files 45.94 MB
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ImmuneCellandToxoData_2.zip
45.89 MB
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README.md
44.97 KB
Abstract
ZBP1 is an innate sensor of nucleic acids in the Z-conformation and regulates immune responses via cell death pathways and NF-kB signaling. Previous work has demonstrated an essential role for ZBP1 in viral restriction, however the role ZBP1 plays in protection against other pathogens is in early stages of exploration. Toxoplasma gondii is an obligate intracellular parasite that can infect all nucleated cells and establishes a chronic infection of the brain, requiring a robust innate and adaptive immune response and multiple cell death pathways for host survival. Importantly, innate sensors of T. gondii infection of the central nervous system are still being defined. Prior work has implicated caspase-1 and caspase-8 in the control of T. gondii in the brain. Because ZBP1 can activate both caspase-1 and caspase-8, we sought to explore the role of ZBP1 during T. gondii infection. During early infection, we found an increase in parasite burden, a decrease in NK1.1+ cell, neutrophil, and monocyte recruitment, and impaired NK1.1+ cell cytokine production in the peritoneum of Zbp1-/- mice. Interestingly, during the early adaptive immune response, the immune cell recruitment defects and impaired parasite control were ameliorated. During the brain stage of infection, ZBP1 regulated parasite restriction and numerous inflammatory responses to infection. Our findings establish ZBP1 as a critical regulator of host defense to T. gondii and highlight the importance of ZBP1 in the development of inflammation during both the acute and chronic infection.
Dataset DOI: 10.5061/dryad.4tmpg4frf
Description of the data and file structure
This dataset was generated as a part of a study examining the role of ZBP1 during Toxoplasma gondii infection. The immune response and control of T. gondii were explored using a mouse model of infection. The dataset contains cell counts and frequencies from flow cytometry experiments, enumeration of parasite, and real time PCR data. The dataset supports a manuscript published in 2026 in Immunohorizons.
Files and variables
File: ImmuneCellandToxoData_2.zip
Description: These files contain raw data and processed data from flow cytometry experiments. The files contain the date, experimental timepoint (DPI refers to days post-infection, naive refers to uninfected), sex of the mice (M or F), the tissues, and some specifics about the experiment. Restim refers to restimulation for intracellular cytokine staining, and NK refers to a panel to identify NK cell markers. Data from real-time PCR experiments measuring gene expression from whole brain or whole tissue RNA is also included. A key is described below for flow cytometry files and real-time PCR files as column headers are used across experiments. Following the key, each file name is listed with a description of the file type and/or descriptions of the column headings in the CSV files.
Key to file type and column headings:
Flow cytometry files
Flow cytometry was performed as described in the methods and detailed in the supplementary figures of the associated manuscript. The column headers describe the gating strategy followed by the statistic that was extracted.
Singlets refers to a singlet gate that approximates a linear relationship of scatter area to scatter height or width. Any cells that deviate from this relationship are often comprised to two or more cells.
Live refers to cells that are negative for a live/dead reagent.
Freq of refers to frequency of a particular gate of a parent population.
CD designation refers to surface markers. The column titles in flow cytometry include gates and gate statistics and are defined in the key below in parentheses
- Singlets.Live.CD4....Freq..of.LiveCD4 (CD4 T cells)
- Singlets.Live.CD4..CD44hiCD62Llo...Freq..of.CD4.CD44hiCD62Llo..CD4. (activated CD4 T cells within CD4)
- Singlets.Live.CD4..CD44hiCD62Llo...Freq..of.LiveCD44hiCD62Llo..CD4. (activated CD4 T cells within all live cells)
- Singlets.Live.CD4..Foxp3...Freq..of.CD4.Foxp3..CD4. (FoxP3 refers to a regulatory
- T cell (Treg) marker. This statistic refers to the frequency of Tregs in the CD4 T cell population)
- Singlets.Live.CD4..Foxp3...Freq..of.LiveFoxp3 (Treg frequency of live cells)
- Singlets.Live.CD8....Freq..of.LiveCD8 (Frequency of CD8 T cells of all live cells)
- Singlets.Live.CD8..CD44hiCD62Llo...Freq..of.CD8.CD44hiCD62Llo..CD8. (frequency of activated CD8 T cells in the CD8 population)
- Singlets.Live.CD8..CD44hiCD62Llo...Freq..of.Live.CD44hiCD62Llo...CD8. (frequency of activated CD8 T cells of all live cells)
- Singlets.Live.CD45hiCD11b....Freq..of.Live.CD45hiCD11b. (Freqency of cells that approximate microglia of all live cells)
- Singlets.Live.CD45hiCD11b..Ly6G....Freq..of.Live.Ly6G. (Frequency of neutrophils of all live cells)
- Singlets.Live.CD45hiCD11b..Ly6G..iNOS...Freq..of.CD45hiCD11b.iNOS..CD45hiCD11b.. (frequency of inducible nitric oxide synthase expressing cells in CD45hiCD11b+Ly6G- population)
- Singlets.Live.CD45hiCD11b..Ly6G..iNOS...Freq..of.LiveiNOS...28 (frequency of iNOS expressing CD45hiCD11b+Ly6G- cells of all live cells)
- Singlets.Live.CD45hiCD11b..Ly6G..Ly6Chi...Freq..of.LiveLy6Chi (Frequency of CD45hiCD11b+Ly6G- cells that highly express Ly6C.
- Singlets.Live.CD45hiCD11b..Ly6G..Ly6Chi...Geometric.Mean..iNOS. (mean fluorescence intensity (MFI) of iNOS expression in CD45hiCD11b+Ly6G- cells)
- Singlets.Live.CD45hiCD11b..Ly6G..Ly6Chi...Geometric.Mean..MHC.II.(MFI of MHC Class II expression on CD45hiCD11b+Ly6G- cells)
- Singlets.Live.CD45intCD11b....Geometric.Mean..MHC.II.(MFI of MHC Class II expression on microglia)
- Singlets.Live.CD45intCD11b..CD11c....Freq..of.CD45intCD11b.CD11c..CD45intCD11b.. (Frequency of microglia that express CD11c)
- Singlets.Live.CD45intCD11b..CD11c....Freq..of.LiveCD11c (Frequency of microglia that express CD11c of all live cells)
- Singlets.Live.B220....Freq..of.Live B220 (B220 expressing cells of all live cells)
- Singlets.Live.CD3..CD8..Ki67....Freq..of.CD8. Ki67..CD8. (Ki67(proliferating) T cells as a frequency of all CD8 T cells)
- Singlets.Live.CD3..CD8..Ki67....Freq..of.Live Ki67...32 (frequency of proliferating CD8 T cells of all live cells)
- Singlets.Live.CD3..Ki67....Freq..of.CD3.Ki67..CD3. (frequency of proliferating CD3+ T cells)
- Singlets.Live.CD3..Ki67....Freq..of.Live Ki67...36 (frequency of proliferating T cells of all live cells)
- Singlets.Live.CD45intCD11b..Ki67....Freq..of.CD45intCD11b.ki67..CD45intCD11b.. (frequency of proliferating microglia of total microglia)
- Singlets.Live.CD45intCD11b..Ki67....Freq..of.Live Ki67...83 (frequency of proliferating microglia of all live cells)
- Singlets.Live.CD45intCD11b..MHCII...Freq..of.CD45intCD11b.MHCII..CD45intCD11b..(frequency of microglia expressing MHC Class II of all microglia)
- Singlets.Live.CD45intCD11b..MHCII...Freq..of.Live MHCII...87 (frequency of microglia expressing MHC Class II of all live cells)
- Singlets.Live.CD45intCD11b..MHCII...Geometric.Mean..MHC.II. (mean fluorescence intensity of MHCII on microglia)
- Singlets.Live.CD3.CD4..Foxp3....Geometric.Mean..IL10. (mean fluorescence intensity of IL-10 in non-Treg CD4 cells)
- Singlets.Live.CD3.CD4..Foxp3....Geometric.Mean..TNFa. (mean fluorescence intensity of TNF (tumor necrosis factor) in non-Treg CD4 cells)
- Singlets.Live.CD3.CD4..Foxp3....Geometric.Mean..IFNg. (mean fluorescence intensity of interferon gamma(IFNg) in non-Treg CD4 cells)
- Singlets.Live.CD3.CD4..Foxp3..IFNg....Freq..of.Foxp3.ifng.foxp3...13 (frequency of IFNg non-Treg of total CD4 T cells)
- Singlets.Live.CD3.CD4..Foxp3..IFNg....Freq..of.Live ifng...15(frequency of IFNg non-Treg of all live cells)
- Singlets.Live.CD3.CD4..Foxp3..IL10....Freq..of.Foxp3.il10.foxp3...17 (frequency of IL-10 producing non-Treg of total CD4 T cells)
- Singlets.Live.CD3.CD4..Foxp3..IL10....Freq..of.Liveil10...19(frequency of IL-10 producing non-Treg of all live cells)
- Singlets.Live.CD3.CD4..Foxp3..TNFa....Freq..of.Foxp3.tnf.foxp3...21(frequency of TNF producing non-Treg of total CD4 T cells)
- Singlets.Live.CD3.CD4..Foxp3..TNFa....Freq..of.Live tnf...23(frequency of TNF-producing non-Treg of all live cells)
- Singlets.Live.CD3.CD8....Geometric.Mean..IL10.(MFI of IL-10 in CD8 T cells)
- Singlets.Live.CD3.CD8....Geometric.Mean..TNFa.(MFI of TNF in CD8 T cells)
- Singlets.Live.CD3.CD8....Geometric.Mean..IFNg.(MFI of IFNg in CD8 T cells)
- Singlets.Live.CD3.CD8..IFNg....Freq..of.CD3.CD8.ilf.cd8 (Frequency of IFNg producing CD8 T cells within CD8 T cells)
- Singlets.Live.CD3.CD8..IFNg....Freq..of.Live ifng...51 (Frequency of IFNg producing CD8 T cells within all live cells)
- Singlets.Live.CD3.CD8..IL10....Freq..of.CD3.CD8. il10.cd8 (Frequency of IL10 producing CD8 T cells within CD8 T cells)
- Singlets.Live.CD3.CD8..IL10....Freq..of.Live il10...55 (Frequency of IL-10 producing CD8 T cells within all live cells)
- Singlets.Live.CD3.CD8..TNFa....Freq..of.CD3.CD8.tnf.cd8 (Frequency of TNF producing CD8 T cells within CD8 T cells)
- Singlets.Live.CD3.CD8..TNFa....Freq..of.Live tnf...59 (Frequency of TNF producing CD8 T cells within all live cells)
- Singlets.Live.Q1..CD3....CD8..Q2..CD11c....MHC.II....Freq..of.Live (Frequency of dendritic cells of all lives cells)
- Singlets.Live.CD11b..CD3.Nk1.1....Freq..of.Live (Natural killer T(NKT) cells as frequency of live cells)
- Singlets.Live.CD11b..CD3.Nk1.1....Geometric.Mean..TNFa. (MFI of TNF in NKT cells)
- Singlets.Live.CD11b..CD3.Nk1.1....Geometric.Mean..IFNg.(MFI of IFNg in NKT cells)
- Singlets.Live.CD11b..CD3.Nk1.1..IFNg....Freq..of.CD3.Nk1.1.(Frequency of IFNg producing NKT cells of total NKT cells)
- Singlets.Live.CD11b..CD3.Nk1.1..IFNg....Freq..of.Live Frequency of IFNg producing NKT cells of live cells)
- Singlets.Live.CD11b..CD3.Nk1.1..Tbet....Freq..of.CD3.Nk1.1.(Frequency of Tbet expression in NKT cells)
- Singlets.Live.CD11b..CD3.Nk1.1..TNFa....Freq..of.CD3.Nk1.1. (Frequency of TNF producing NKT cells of total NKT cells)
- Singlets.Live.CD11b..CD3.Nk1.1..TNFa....Freq..of.Live (Frequency of TNF producing NKT cells of total NKT cells)
- Singlets.Live.CD19....Freq..of.Live (B cells of all live cells)
- Singlets.Live.CD19....Geometric.Mean..TNFa. (MFI of TNF is B cells)
- Singlets.Live.CD19....Geometric.Mean..IFNg. (MFI of IFNg in B cells)
- Singlets.Live.CD19..IFNg....Freq..of.CD19. (Frequency of IFNg-producing B cells of all B cells)
- Singlets.Live.CD19..IFNg....Freq..of.Live (Frequency of IFNg-producing B cells of all live cells)
- Singlets.Live.CD19..IFNg....Geometric.Mean..IFNg.(MFI of IFNg in B cells)
- Singlets.Live.CD19..TNFa....Freq..of.CD19. (Frequency of TNF-producing B cells of all B cells)
- Singlets.Live.CD19..TNFa....Freq..of.Live (Frequency of TNF-producing B cells of all live cells)
- Singlets.Live.CD19..TNFa....Geometric.Mean..TNFa.(MFI of TNF in B cells)
- Singlets.Live.CD3..CD4..Tbet....Geometric.Mean..Tbet. (MFI of T bet expression in CD4 T cells)
- Size.Singlets.Live.IL12....Freq..of.Live (Frequency of IL-12 producing cells in all live cells)
- Cell.number (number of cells counted per sample by hemacytometer count)
- Size.Singlets.Live.IL12..Lineage..CD64....Freq..of.IL12.(Frequency of IL-12 producing macrophages of all IL-12 producers)
- Size.Singlets.Live.IL12..Lineage..CD64....Freq..of.Live.(Frequency of IL-12 producing macrophages of all live cells)
- Size.Singlets.Live.IL12..Lineage..CD64..Q1..MHC.II....CD11c....Freq..of.IL12.(Frequency of dendritic cells making IL-12 of all IL-12 producing cells)
- Size.Singlets.Live.IL12..Lineage..CD64..Q1..MHC.II....CD11c....Freq..of.
- Singlets.Live.Lin..CD64..CD11c.MHCII....Geometric.Mean..IL12.(MFI of IL-12 in dendritic cells)
Real time PCR files have the following column headings defined below in parentheses
- Well
- Fluor (fluorescent probe detected)
- Target (gene target)
- Content (sample or empty)
- Sample (sample name)
- Biological.Set.Name (name of group of replicates)
- Cq (quantification cycle aka threshold)
- Cq.Mean (average Cq across replicates)
- Cq.Std..Dev (standard deviate of Cq values across replicates)
- Starting.Quantity..SQ.(quantity of DNA estimated from a standard curve)
- Log.Starting.Quantity
- SQ.Mean (mean of DNA quantities across replicates)
- SQ.Std..Dev (standard deviation of DNA quantities across replicates
/2023_11_16- ZBP1 28 dpi M/Brain ZBP1 111623.csv
- Flow cytometry file see key above
/2023_11_16- ZBP1 28 dpi M/DNA Quantification Brain 12.7.23 ZBP and APOE.csv
- Dilution.500ng.8.5uL
- ul.DNA (volume of DNA extract added to sample)
- ul.H20 (volume of water added to each sample)
/2023_11_16- ZBP1 28 dpi M/Harris Lab _20231208_100907_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real Time PCR file
/2023_11_16- ZBP1 28 dpi M/Harris Lab _20231211_103148_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real Time PCR file
/2023_11_16- ZBP1 28 dpi M/RNA Quantification Brain 12.7.23 ZBP and APOE.csv
- ug.ul (concentration in micrograms per microliter)
- dilution..2ug.10ul. (volume to dilute to the given concentration)
- X35ul.sample
- h2o (amount of water added to each sample)
/2023_11_16- ZBP1 28 dpi M/Spleen cells 4wpi M 111623.csv
- Flow cytometry file described above
/2023_11_20- ZBP1 12 dpi F/Brain Cells.csv
- Flow cytometry file described above
/2023_11_20- ZBP1 12 dpi F/Spleen Cells.csv
- Flow cytometry file described above
/2023_11_20- ZBP1 28 dpi F/ZBP1 Brain Cells 4wpi 112023.csv
- Flow cytometry file described above
/2023_11_20- ZBP1 28 dpi F/ZBP1 Spleen Cells 4wpi 112023.csv
- Flow cytometry file described above
/2023_12_06- ZBP1 28 dpi M restim/BFA- Brain.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2023_12_06- ZBP1 28 dpi M restim/BFA- Spleen.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2023_12_06- ZBP1 28 dpi M restim/Brain DCs.csv
- Flow cytometry file described above
/2023_12_06- ZBP1 28 dpi M restim/Harris Lab
- Flow cytometry file described above
_20240214_112629_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR as described above
/2023_12_06- ZBP1 28 dpi M restim/PMA- Brain.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2023_12_06- ZBP1 28 dpi M restim/PMA- Spleen.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2023_12_06- ZBP1 28 dpi M restim/ZBP1 120823 Brain no stim.csv
- Flow cytometry file described above
/2023_12_06- ZBP1 28 dpi M restim/ZBP1 120823 Spleen no stim.csv
- Flow cytometry file described above
/2024_01_03- ZBP1 12 dpi F/Brain 12dpi 010324-1.csv
- Flow cytometry file described above
/2024_01_03- ZBP1 12 dpi F/Spleen 12d[pi 010324.csv
- Flow cytometry file described above
/2024_01_17- ZBP1 8 dpi M restim/BFA- PEC.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_01_17- ZBP1 8 dpi M restim/myeloid redo.csv
- Flow cytometry file described above
/2024_01_17- ZBP1 8 dpi M restim/PEC BFA Foxp3.csv
- Flow cytometry file described above
/2024_01_17- ZBP1 8 dpi M restim/PEC CD4 Tbet no stim 011724.csv
- Flow cytometry file described above
/2024_01_17- ZBP1 8 dpi M restim/PEC no stim 011724.csv
- Flow cytometry file described above /2024_01_17- ZBP1 8 dpi M restim/PEC PMA Foxp3.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_01_17- ZBP1 8 dpi M restim/PMA- PEC 011724.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_01_17- ZBP1 8 dpi M restim/Spleen BFA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)\
/2024_01_17- ZBP1 8 dpi M restim/Spleen no stim 011724.csv
- Flow cytometry file described above /2024_01_17- ZBP1 8 dpi M restim/Spleen PMA Foxp3.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_01_17- ZBP1 8 dpi M restim/Spleen PMA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_01_17- ZBP1 8 dpi M restim/Zbp1 8 dpi myeloid redo 1.17.24.csv
- Flow cytometry file described above
/2024_01_17- ZBP1 8 dpi M restim/ZBP1 8dpi IFNg 05.08.24.csv
- Flow cytometry file described above
/2024_01_19- ZBP1 28 dpi M restim/BFA- Brain.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)\
/2024_01_19- ZBP1 28 dpi M restim/BFA- Spleen.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)\
/2024_01_19- ZBP1 28 dpi M restim/Brain no stim 011724-1.csv
- Flow cytometry file described above
/2024_01_19- ZBP1 28 dpi M restim/Brain no stim 011724.csv
- Flow cytometry file described above
/2024_01_19- ZBP1 28 dpi M restim/PMA- Brain.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_01_19- ZBP1 28 dpi M restim/PMA- Spleen.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_01_19- ZBP1 28 dpi M restim/Spleen no stim 011724.csv
- Flow cytometry file described above
/2024_01_19- ZBP1 28 dpi M restim/ZBP1 28dpi Brain DCs 1.19.24.csv
- Flow cytometry file described above
/2024_01_21- ZBP1 F 12 dpi/ZBP1 Brain 12dpi 012424.csv
- Flow cytometry file described above\
/2024_01_21- ZBP1 F 12 dpi/ZBP1 Spleen 12dpi 012424.csv
- Flow cytometry file described above
/2024_02_06- ZBP1 F 5 dpi/IL12 population 2.6.24.csv
- Flow cytometry file described above
/2024_02_06- ZBP1 F 5 dpi/IL12 populations redo final.csv
- Flow cytometry file described above
/2024_02_06- ZBP1 F 5 dpi/IL12 populations redo.csv
- Flow cytometry file described above
/2024_02_06- ZBP1 F 5 dpi/IL12 populations redone.csv
- Flow cytometry file described above
/2024_02_06- ZBP1 F 5 dpi/PEC IL12 cells.csv
- Flow cytometry file described above
/2024_02_06- ZBP1 F 5 dpi/Spleen IL12 cells.csv
- Flow cytometry file described above
/2024_02_09- ZBP1 8 dpi restim M/PEC no stim 020924.csv
- Flow cytometry file described above
/2024_02_09- ZBP1 8 dpi restim M/PEC- BFA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_02_09- ZBP1 8 dpi restim M/PEC- PMA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_02_09- ZBP1 8 dpi restim M/Spleen no stim 020924.csv
- Flow cytometry file described above
/2024_02_09- ZBP1 8 dpi restim M/Spleen- BFA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_02_09- ZBP1 8 dpi restim M/ZBP1 myeloid redo 2.9.24.csv
- Flow cytometry file described above
/2024_02_13- ZBP1 F 5 dpi/IL12 populations .csv
- Flow cytometry file described above
/2024_02_13- ZBP1 F 5 dpi/Spleen IL12 021324.csv
- Flow cytometry file described above
/2024_02_13- ZBP1 F 5 dpi/ZBP1 5dpi IL12 ELISA 05.07.24.csv
- ELISA data for IL-12
/2024_04_05- ZBP1 7 dpi ZsGreen pilot/ZBP1 7dpi ZsGreen Pilot 040524.csv
- Flow cytometry file described above
- ZsGreen refers to cells with cre-recombinase activity after infection with T. gondii expressing cre and reflects infected cells
/2024_04_08- ZBP1 F 5dpi/IL12 populations redo.csv
- Flow cytometry file described above
/2024_04_08- ZBP1 F 5dpi/PECS 040824.csv
- Flow cytometry file described above
/2024_04_08- ZBP1 F 5dpi/PECS IL12 catagories.csv
- Flow cytometry file described above
/2024_04_08- ZBP1 F 5dpi/Spleen 0408024.csv
- Flow cytometry file described above
/2024_04_11- ZBP1 8 dpi restim M/IFNg populations PECs BFA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_04_11- ZBP1 8 dpi restim M/IFNg populations PECs PMA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_04_11- ZBP1 8 dpi restim M/PECs no stim 041124.csv
- Flow cytometry file described above
/2024_04_11- ZBP1 8 dpi restim M/PECs- BFA 041124.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_04_11- ZBP1 8 dpi restim M/PECs- PMA 041124.csv
- Flow cytometry file described above
/2024_04_11- ZBP1 8 dpi restim M/Spleen no stim 041124.csv
- Flow cytometry file described above
/2024_04_11- ZBP1 8 dpi restim M/Spleen- BFA 041124.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_04_11- ZBP1 8 dpi restim M/Spleen- PMA 041124.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_04_11- ZBP1 8 dpi restim M/ZBP1 myeloid redo 4.1..24.csv
- Flow cytometry file described above
/2024_05_29- ZBP1 TFcre 28 dpi/ZBP1 brain immune populations 05.29.24.csv
- Flow cytometry file described above
/2024_05_29- ZBP1 TFcre 28 dpi/ZBP1 Brain TFcre 052924.csv
- Flow cytometry file described above
/2024_06_13- ZBP1 TFcre 42 dpi/Brain TFcre ZBP1 061324.csv
- Flow cytometry file described above
/2024_10_10- ZBP1 M 8dpi restim/IFNg PEC- BFA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_10_10- ZBP1 M 8dpi restim/IFNg PEC- PMA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 8 dpi myeloid redo 10.10.24.csv
- Flow cytometry file described above
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 M 8dpi restim cell counts 10.10.24.csv
- PECs = peritoneal exudate cells
- Average= average number of cells
- X1sq
- x100.000= dilution factor
- X1ml
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 PECs BFA 10.10.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 PECs no stim 10.10.24.csv
- Flow cytometry file described above
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 PECs PMA 10.10.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 Spleen BFA 10.10.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 Spleen no stim 10.10.24.csv
- Flow cytometry file described above
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 Spleen PMA 10.10.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_10_10- ZBP1 M 8dpi restim/ZBP1 Spleen- PMA 10.10.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_10_7- ZBP1 F 5dpi NK cells/Harris Lab _20241022_093818_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR as described in key
/2024_10_7- ZBP1 F 5dpi NK cells/Lydia Sibley_20241206_152217_796BR02044_ADMIN - Quantification Cq Results.csv
- Real time PCR as described in key
/2024_10_7- ZBP1 F 5dpi NK cells/PECs IFNg BFA.csv
- Flow cytometry file described above
/2024_10_7- ZBP1 F 5dpi NK cells/PECs NK cell regate 10.7.24.csv
- Flow cytometry file described above
/2024_10_7- ZBP1 F 5dpi NK cells/PECs no stim myeloid redo 10.7.24.csv
- Flow cytometry file described above
/2024_10_7- ZBP1 F 5dpi NK cells/PECs PMA myeloid TNF 10.7.24.csv
- Flow cytometry file described above
/2024_10_7- ZBP1 F 5dpi NK cells/Table.csv
- Flow cytometry file described above
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 5dpi ELISA stats.csv
- Date = date of experiment
- Group = genotype
- Ifng = cytokine measured
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 5dpi IFNg ELISA 10.22.24.csv
- ELISA data
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 5dpi PECs RNA 10.7.24.csv
Spectrophotometry data of RNA samples
- Sample.Read.
- Well.ID
- Name
- Location
- X260.Raw
- X280.Raw
- X320.Raw
- X260
- X280
- X260.280
- ng.µL
- ug.ul
- dilution..2ug.10ul.
- X15ul.sample
- h2o
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 cell counts 10.7.24.csv
- PECs=peritoneal exudate cells
- Average= cell counts
- X1sq
- x100.000=dilution factor
- X1ml
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 IFNg ELISA sorted 10.7.24.csv
- ELISA data
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 PECs 5dpi 10.7.24.csv
- Flow cytometry file described above
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 PECs BFA 10.7.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 PECs PMA 10.7.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 Spleen 5dpi 10.7.24.csv
- Flow cytometry file described above
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 Spleen BFA 10.7.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 Spleen PMA 10.7.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_10_7- ZBP1 F 5dpi NK cells/ZBP1 Spleen redo 10.7.24.csv
- Flow cytometry file described above
/2024_11_12- ZBP1 5dpi NK cells/PECs no stim Ly6C regate 11.18.25.csv
- Flow cytometry file described above
/2024_11_12- ZBP1 5dpi NK cells/PECs PMA Myeloid TNF 11.12.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi cell counts 11.12.24.csv
- PECs = peritoneal exudate cells
- Average= average of cell counts
- X1sq
- x100.000= dilution factor
- X1ml
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi IL12 PEC fluid 01.14.25.csv
- IL-12 ELISA data
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi PECs BFA 11.12.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi PECs no stim 11.12.24.csv
- Flow cytometry file described above
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi PECs PMA 11.12.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi Spleen BFA 11.12.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi Spleen no stim 11.12.24.csv
- Flow cytometry file described above
/2024_11_12- ZBP1 5dpi NK cells/ZBP1 5dpi Spleen PMA 11.12.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_11_13- ZBP1 M naive/ZBP1 naive Blood 11.13.24.csv
- Flow cytometry file described above
/2024_11_13- ZBP1 M naive/ZBP1 naive Bone Marrow 11.13.24.csv
- Flow cytometry file described above
/2024_11_13- ZBP1 M naive/ZBP1 naive cell counts 11.13.24.csv
- Blood= blood sample
- Average= average cell counts
- X1sq
- x100.000=dilution factor
- X500ul
/2024_11_13- ZBP1 M naive/ZBP1 naive Liver 11.13.24.csv
- Flow cytometry file described above
/2024_11_13- ZBP1 M naive/ZBP1 naive Lymph Nodes 11.13.24.csv
- Flow cytometry file described above
/2024_11_13- ZBP1 M naive/ZBP1 naive PECs 11.13.24.csv
- Flow cytometry file described above
/2024_11_13- ZBP1 M naive/ZBP1 naive Spleen 11.13.24.csv
- Flow cytometry file described above
/2024_11_18- ZBP1 5dpi NK cells/IFNg PECs BFA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_11_18- ZBP1 5dpi NK cells/IFNg PECs PMA.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_11_18- ZBP1 5dpi NK cells/PECS PMA CD11b TNF redo.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_11_18- ZBP1 5dpi NK cells/PECS redo CD11b gating 11.18.25.csv
- Flow cytometry file described above
/2024_11_18- ZBP1 5dpi NK cells/Spleen- BFA live-1.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi Cell Counts 11.18.24.csv
- Average = average of counts
- X1sq
- x100.000 = dilution factor
- X1.ml
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi IFNg ELISA 11.2..24.csv
- IFNg ELISA data
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi PECs BFA 11.18.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi PECs no stim 11.18.24.csv
- Flow cytometry file described above
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi PECs PMA 11.18.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi Spleen BFA 11.18.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi Spleen no stim 11.18.24.csv
- Flow cytometry file described above
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi Spleen PMA 11.18.24.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2024_11_18- ZBP1 5dpi NK cells/ZBP1 5dpi TNF ELISA 11.22.24.csv
- TNF ELISA data
/2024_12_12- ZBP1 M naive/ZBP1 naive M Blood 12.12.24.csv
- Flow cytometry file described above
/2024_12_12- ZBP1 M naive/ZBP1 naive M Bone Marrow 12.12.24.csv
- Flow cytometry file described above
/2024_12_12- ZBP1 M naive/ZBP1 naive M Cervical Lymph Nodes 12.12.24.csv
- Flow cytometry file described above
/2024_12_12- ZBP1 M naive/ZBP1 naive M Liver 12.12.24.csv
- Flow cytometry file described above
/2024_12_12- ZBP1 M naive/ZBP1 naive M PECs 12.12.24.csv
- Flow cytometry file described above
/2024_12_12- ZBP1 M naive/ZBP1 naive M Spleen 12.12.24.csv
- Flow cytometry file described above
/2025_01_21- ZBP1 5 dpi M UMAP/Blood.csv
- Flow cytometry file described above
/2025_01_21- ZBP1 5 dpi M UMAP/Harris Lab _20250127_120829_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_01_21- ZBP1 5 dpi M UMAP/Harris Lab _20250521_151813_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_01_21- ZBP1 5 dpi M UMAP/PECs BFA 1.21.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2025_01_21- ZBP1 5 dpi M UMAP/PECs PMA 1.21.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_01_21- ZBP1 5 dpi M UMAP/PECs.csv
- Flow cytometry file described above
/2025_01_21- ZBP1 5 dpi M UMAP/Table.csv
- Flow cytometry file described above
/2025_01_21- ZBP1 5 dpi M UMAP/ZBP1 5dpi PECs 1.21.25.csv
- Flow cytometry file described above
/2025_01_21- ZBP1 5 dpi M UMAP/ZBP1 5dpi PECS PMA 1.21.25.csv
- Flow cytometry file described above
/2025_01_21- ZBP1 5 dpi M UMAP/ZBP1 cell counts 1.21.25.csv
- PECS = peritoneal exudate cells
- Average = average count per square
- X1.sq
- x100.000=dilution factor
- X500ul
/2025_02_03- ZBP1 5 dpi NK M/Harris Lab _20250225_095309_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_02_03- ZBP1 5 dpi NK M/ZBP1 Cell counts 2.3.25.csv
- PECS = peritoneal exudate cells
- Average = average count per square
- X1.sq
- x100.000 = dilution factor
- X500ul
/2025_02_18- Casp8 5 dpi NK cell restim/Casp8 5dpi PECs BFA 2.18.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2025_02_18- Casp8 5 dpi NK cell restim/Casp8 5dpi PECs PMA 2.18.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_02_18- Casp8 5 dpi NK cell restim/Casp8 5dpi PECs PMA Eomes 2.18.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_02_18- Casp8 5 dpi NK cell restim/Casp8Ripk3 PECs 5dpi no stim 2.18.25.csv
- Flow cytometry file described above
/2025_02_18- Casp8 5 dpi NK cell restim/IFNg elisa ZBP1 8dpi Casp1 and Casp8 5dpi 3.14.25.csv
- IFNg ELISA data
/2025_02_18- Casp8 5 dpi NK cell restim/Myeloid redo 125.25.csv
- Flow cytometry file described above
/2025_02_18- Casp8 5 dpi NK cell restim/PEC neutrophils.csv
- Flow cytometry file described above
/2025_03_10- Casp1 5 dpi NK/Casp1 PECS BFA 3.10.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2025_03_10- Casp1 5 dpi NK/Casp1 PECS no stim 3.10.25.csv
- Flow cytometry file described above
/2025_03_10- Casp1 5 dpi NK/Casp1 PECs PMA 3.10.25 redo.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_03_10- Casp1 5 dpi NK/Casp1 PECs PMA 3.10.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_03_10- Casp1 5 dpi NK/Harris Lab _20250319_112643_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_03_10- Casp1 5 dpi NK/IFNg elisa ZBP1 8dpi Casp1 and Casp8 5dpi 3.14.25.csv
- IFNg ELISA
/2025_03_10- Casp1 5 dpi NK/Myeloid regate 12.5.25.csv
- Flow cytometry file described above
/2025_04_02- ZBP1 28 dpi F IL1a release/ZBP1 IL1a release 4.2.25.csv
- IL-1alpha ELISA
/2025_05_01- ZBP1 28 dpi F IL1a release/Harris Lab _20250508_132008_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_05_01- ZBP1 28 dpi F IL1a release/ZBP1 IL1a release 5.1.25.csv
- IL-1alpha ELISA
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 5dpi cell counts 5.6.25.csv
- PECs = peritoneal exudate cells
- Average = average cell per square
- X1sq
- x100.000=dilution factor
- X1ml
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 5dpi PECs BFA 5.6.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 5dpi PECs NK 5.6.25.csv
- Flow cytometry file described above
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 5dpi PECs PMA 5.6.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 5dpi Spleen BFA 5.6.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 5dpi Spleen NK 5.6.25.csv
- Flow cytometry file described above
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 5dpi Spleen PMA 5.6.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_05_06- Casp8 5 dpi NK cell restim/Casp8 and Casp1 5dpi DNA 7.8.25.csv
- Date = experimental date
- Time.point = day post-infection
- Tissue = tissue
- Sample = genotype and number
- ug.ul =concentration
- Dilution.500ng.8.5uL
- ul.DNA =volume of DNA per sample
- ul.H20 =volume of water per sample
/2025_05_06- Casp8 5 dpi NK cell restim/Harris Lab _20250708_125124_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_05_06- Casp8 5 dpi NK cell restim/IFNg elisa Casp1 and Casp8 5dpi 7.9.25.csv
- IFNg ELISA
/2025_05_06- Casp8 5 dpi NK cell restim/Myeloid redo 12.5.25.csv
- Flow cytometry file described above
/2025_05_07-ZBP1 F 28 dpi IL1a release/Harris Lab _20250514_142759_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_05_08- ZBP1 28 dpi M restim/ZBP1 28dpi M Brain BFA 5.8.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2025_05_08- ZBP1 28 dpi M restim/ZBP1 28dpi M Brain PMA 5.8.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_05_08- ZBP1 28 dpi M restim/ZBP1 28dpi M cell counts 5.8.25.csv
- Cell count data
/2025_05_08- ZBP1 28 dpi M restim/ZBP1 28dpi M Spleen BFA 5.8.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Brefeldin A (BFA)
/2025_05_08- ZBP1 28 dpi M restim/ZBP1 28dpi M Spleen PMA 5.8.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_05_27- ZBP1 5 dpi M IL1b ex vivo release/Harris Lab _20250605_113123_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_05_27- ZBP1 5 dpi M IL1b ex vivo release/ZBP1 IL1b release 5dpi 5.27.25.csv
- IL-1beta ELISA
/2025_07_07- Casp1 5 dpi M restim/Casp1 5dpi IL12 elisa 7.15.25.csv
- IL_12p40 ELISA
/2025_07_07- Casp1 5 dpi M restim/Casp1 5dpi PECs 7.7.25.csv
- Flow cytometry file described above
/2025_07_07- Casp1 5 dpi M restim/Casp1 5dpi PECs PMA 7.7.25.csv
- Flow cytometry file described above
- Restim refers to ex vivo restimulation of cells with Phorbol 12- myristate 13-acetate (PMA)
/2025_07_07- Casp1 5 dpi M restim/Myeloid redo 12.5.25.csv
- Flow cytometry file described above
/2025_12_09- 5 dpi NK identification/Copy of 12.17.25 Lydia Zbp1 peripheral gDNA + Abbe GFAP brain.csv
- Real time PCR data described in key
/2025_12_09- 5 dpi NK identification/Harris Lab _20260115_142503_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/2025_12_09- 5 dpi NK identification/Table.csv
- Flow cytometry file described above
/2025_12_09- 5 dpi NK identification/ZBP1 5dpi IL1a release 12.9.25.csv
- IL-1alpha ELISA
/2025_12_09- 5 dpi NK identification/ZBP1 5dpi ILC IFNg 12.9.25.csv
- Flow cytometry file described above
/2025_12_09- 5 dpi NK identification/ZBP1 5dpi M PECs NK cell identification 12.9.25 .csv
- Flow cytometry file described above
/2025_12_09- 5 dpi NK identification/ZBP1 5dpi peripheral tissues 1.6.26 retry.csv
/2025_12_09- 5 dpi NK identification/ZBP1 5dpi peripheral tissues 1.6.26.csv
/2025_12_12- ZBP1 8dpi IL1a release/ZBP1 8dpi IL1a release 12.12.25.csv
- IL-1alpha ELISA
/Compiled/12 dpi/Harris Lab _20250122_102436_796BR20167_Harris Lab - Quantification Cq Results.csv
- Date = experimental date
- Group = genotype
- ccr2
- ccl2
- cxcl9
- cxcl10
- cxcl2
- cxc1
- ifng
/Compiled/12 dpi/Harris Lab _20250205_131819_796BR20167_Harris Lab - Quantification Cq Results copy.csv
- Real time PCR data described in key
/Compiled/12 dpi/Harris Lab _20250205_131819_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/Compiled/12 dpi/ZBP1_brain_parasite_12dpi.csv
- Date = experimental date
- Genotype = wildtype or zbp1 knockout
- Parasite = cyst burden brain
- iNOS
- Foxp3
- Ly6Chi
- iNOS_Freq
/Compiled/28 dpi/Harris Lab _20250205_110039_796BR20167_Harris Lab - Quantification Cq Results copy.csv
- Real time PCR data described in key
/Compiled/28 dpi/Harris Lab _20250205_110039_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/Compiled/28 dpi/Harris Lab _20251204_134412_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/Compiled/28 dpi/Harris Lab_20250423_152742_796BR02044_Guest - Quantification Cq Results.csv
- Real time PCR data described in key
/Compiled/28 dpi/IHC/ZBP1 28dpi staining 5.27.25.csv
/Compiled/28 dpi/IL1a_release_stats.csv
- Group
- Date = experimental date
- IL1a_release
- max_IL1a_release
- The below are all genes measured by qPCR
- il1a
- il1b
- il1r1
- Icam1
- Vcam1
- Ifng
- Tnf
- Ccr2
- Ccl2
- nos
- Gbp2
- Irga6
- Irgb6
/Compiled/28 dpi/Lydia Sibley_20250129_124526_796BR02044_Guest - Quantification Cq Results copy.csv
- Real time PCR data described in key
/Compiled/28 dpi/Lydia Sibley_20250129_124526_796BR02044_Guest - Quantification Cq Results.csv
- Real time PCR data described in key
/Compiled/28 dpi/ZBP1 28 genes.csv
- Date
- Group
- cxcl1
- cxcl2
/Compiled/28 dpi/ZBP1 4wpi Stats.csv
- Date
- Group
- Cysts
- Ly6G
- Ly6Chi
- iNOS
- CD4
- CD8
- BFA_CD4
- BFA_CD4_Freq
- BFA_CD4_IFNg
- BFA_CD4_IFNg_Freq
- BFA_CD4_TNFa
- BFA_CD4_TNFa_Freq
- BFA_CD8
- BFA_CD8_Freq
- BFA_CD8_IFNg
- BFA_CD8_IFNg_Freq
- BFA_CD8_TNFa
- BFA_CD8_TNFa_Freq
- PMA_CD4
- PMA_CD4_IFNg
- PMA_CD4_TNFa
- PMA_CD8
- PMA_CD8_IFNg
- PMA_CD8_TNFa
- IL10
- Foxp3
- PMA_CD4_IFNg_Freq
- PMA_CD4_TNFa_Freq
- PMA_CD8_IFNg_Freq
- PMA_CD8_TNFa_Freq
/Compiled/28 dpi/Zbp1 PMA Frequencies .csv
- CD4.IFNg
- CD4...3
- CD4.IFNg..
- CD8.IFNg
- CD8...7
- CD8.IFNg..
- CD4.TNFa
- CD4...11
- CD4.TNFa..
- CD8.TNFa
- CD8...15
- CD8.TNFa..
/Compiled/5 dpi/Casp1 5dpi Stats.csv
- Group
- Date
- Parasite
- Ly6G
- Ly6ChiMHCII
- NKIFNg
- IFNg_serum
- IFNg_PEC
- IL12_Serum
- IL12_PEC
- Ly6G_redo
- Ly6Chi_redo
/Compiled/5 dpi/Casp8 5dpi Stats.csv
- Date
- Group
- Parasite
- NK
- NK_IFNg
- Ly6G
- Ly6C
- IFNg_Serum
- IFNg_PEC
- Ly6Credo
/Compiled/5 dpi/IL12 redo stats.csv
- Group
- Date
- Lineage. (exclusion of B, T, and NK cells)
- CD64.
- CD64.CD11c.MHCII.
- CD64.CD11c.MHCII..1
- CD64.CD11c.MHCII..2
- CD64.CD11c.MHCII..3
- Lineage.freq
- CD64.freq
- CD64.CD11c.MHCII.freq
- CD64.CD11c.MHCII.freq.1
- CD64.CD11c.MHCII.freq.2
- CD64.CD11c.MHCII.freq.3
/Compiled/5 dpi/ZBP1 5dpi IL18 2.5.25.csv
- IL-18 ELISA
/Compiled/5 dpi/ZBP1 5dpi IL18 ELISA 2.5.25.csv
-
IL-18 ELISA
/Compiled/5 dpi/ZBP1 5dpi parasite .csv -
Date
-
Group
-
IFNg_S = serum
-
IL12_Serum
/Compiled/5 dpi/ZBP1 5dpi spleen .csv
- Date
- Group
- DC_IL12=dendritic cell IL-12
/Compiled/5 dpi/ZBP1_5dpi_genes.csv
- Date
- Group
- Cxcl1
- Cxcl2
- Ccl2
- Ccr2
/Compiled/8 dpi/IFNg elisa ZBP1 8dpi Casp1 and Casp8 5dpi 3.14.25.csv
- IFNg ELISA
/Compiled/8 dpi/IL12 and IL18 ELISA template.csv
- IL.12
- Fluid..1.30 = peritoneal fluid
- Serum..1.50 = serum
/Compiled/8 dpi/NK IFNg Stats.csv
- Date
- Group
- NK
- NK_IFNg
- NK_IFNg_Freq
/Compiled/8 dpi/ZBP1 8 dpi IL-12 5.13.25.csv
- IL-12 ELISA
/Compiled/8 dpi/ZBP1 8 dpi IL-18 5.15.25.csv
- IL-18 ELISA
/Compiled/8 dpi/ZBP1 8dpi stats.csv
- Date
- Group
- CD4
- CD4_IFNg
- CD4_IFNg_Freq
- CD4_TNFa
- CD8
- CD8_IFNg
- CD8_IFNg_Freq
- CD8_TNFa
- NK
- NK_IFNg
- NK_IFNg_Freq
- NK_TNFa
- CD3NK
- CD3NK_IFNg
- CD3NK_IFNg_Freq
- CD3NK_TNF
- Ly6G
- Ly6Chi
- iNOS
- B220
- IL12_serum
- IL12_outliers (data points excluded based on outlier test)
- IL18_serum
- IFNg_serum
- PEC_Parasite (PEC=peritoneal exudate cell)
- B_Parasite (B=brain)
/Compiled/Harris Lab _20250625_120039_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in key
/Compiled/Naive/ZBP1 naive blood.csv
- Date
- Group
- B220
- CD45CD11b
- Ly6G
- TCRb = beta chain of T cell receptor
- CD4
- CD8
- TCRbNK1 = natural killer T cells
- NK1
/Compiled/Naive/ZBP1 naive bone marrow.csv
- Date
- Group
- B220
- CD45CD11b
- Ly6G
- TCRb
- CD4
- CD8
- TCRbNK1
- NK1
/Compiled/Naive/ZBP1 naive liver.csv
- Date
- Group
- B220
- CD45CD11b
- Ly6G
- TCRb
- CD4
- CD8
- TCRbNK1
- NK1
/Compiled/Naive/ZBP1 naive lymph nodes.csv
- Date
- Group
- B220
- CD45CD11b
- Ly6G
- TCRb
- CD4
- CD8
- TCRbNK1
- NK1
/Compiled/Naive/ZBP1 naive PECs.csv
- Date
- Group
- B220
- CD45CD11b
- Ly6G
- TCRb
- CD4
- CD8
- TCRbNK1
- NK1
/Compiled/Naive/ZBP1 naive spleen.csv
- Date
- Group
- B220
- CD45CD11b
- Ly6G
- TCRb
- CD4
- CD8
- TCRbNK1
- NK1
/Compiled/Publication/ZBP1 Source Data.csv
- Experiment.Date
- Genotype
- Nk1.1.IFNg.(number of IFNg producing NK cells)
- Nk1.1.IFNg..Frequency (frequency of IFNg producing NK cells)
- CD4.IFNg. (number of CD4 T cells making IFNg)
- CD4.IFNg..Frequency (frequency of CD4 T cells making IFNg)
- CD8.IFNg. (number of CD8 T cells making IFNg)
- CD8.IFNg..Frequency (frequency of CD8 T cells making IFNg)
/Compiled/Time course 6.30.25 Harris Lab _20250630_103326_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in the key
/Compiled/ZBP1 expression time course Harris Lab _20250328_122828_796BR20167_Harris Lab - Quantification Cq Results.csv
- Real time PCR data described in the key
Code/software
All files are .csv and do not require special software.
Animals
WT (C57BL/6J) (#000664), Casp1-/- (#32662)58, and CBA/J (#000656) strains were obtained from The Jackson Laboratory. Swiss Webster (SW) strains were purchased from Taconic. Zbp1-/-^^ (C57BL/6JCya-Zbp1em1/Cya mice (Catalog S-KO-11088)) mice were provided by John R. Lukens purchased from Cyagen Biosciences (Strain number KOCMP-58203-Zbp1-B6J-VA). Casp8-/-Ripk3-/- and Casp8+/-Ripk3-/- mice were provided by John R. Lukens.59; 60 All mice were maintained within our animal facility. All animal care and use procedures were approved by and conducted in accordance with the University of Virginia’s Institutional Animal Care and Use Committee (IACUC) (protocol number 3968).
Parasite and Infection
To maintain the type II strain Me49 T. gondii line, Swiss Webster were chronically infected (2–6 months), and the parasite was passaged through CBA/J mice for experimental infections. Brains of CBA/J mice (infected 3–8 weeks) were collected in 3 mL of 1X PBS (Gibco Cat#14190144) and homogenized through an 18G needle and then a 22G needle (BD Cat#305195, BD Cat#305155). Tissue cysts were enumerated by mounting 30 μl of brain homogenate on a microscope slide and counting cysts visually on a DM 2000 LED brightfield microscope (Leica). Brain homogenate was diluted to a concentration of 10 tissue cysts of Me49 in 200 μl of 1X PBS. Experimental mice were inoculated by intraperitoneal (i.p.) injection.
Tissue processing
Mice were euthanized by CO2 asphyxiation at specified days post-infection. Peritoneal exudate cells and fluid were collected by injecting 5 mL of cold 1X PBS through the intact peritoneal membrane with a 27G needle (BD Cat#305109), massaging the abdomen, and removing the 1X PBS through the intact peritoneal membrane with a 27G needle. Peritoneal lavage fluid was centrifuged at 1500 RPM for 5 mins to pellet cells. Cells were then resuspended in complete RPMI media (cRPMI) [10% FBS (Gibco Cat#10082-147), 1% penicillin/streptomycin (Gibco Cat#15140-122), 1% sodium pyruvate (Gibco Cat#11360-070), 1% non-essential amino acids (Gibco Cat#11140-050), and 0.1% 2-mercaptoethanol (Gibco Cat#21985-023)]. Remaining peritoneal lavage fluid was stored at -20° C. Cardiac puncture using a 27G needle was used for blood collection. Blood was stored overnight at 4° C, then centrifuged at 20,000 x g for 20 minutes at 4° C to separate serum (Eppendorf 5425 R). Serum was stored at -20° C. For the collection of the brain and/or spleen, transcardiac perfusion with 20 mL cold 1X PBS was performed. Brains and spleens collected for flow cytometry were put into 3 mL cold cRPMI. Brains were homogenized with an 18G needle, and 500 μL of homogenate was stored at -20° C for RNA and DNA extraction as well as cyst counting. Remaining brain homogenate was enzymatically digested with 0.227 mg/mL collagenase/dispase (Sigma/Aldrich Cat#10269638001) and 50 U/mL DNase (Sigma-Aldrich Cat#11284932001) at 37° C for 45 min with inversion of the tubes every 15 min. Post digestion, brain homogenate was passed through a 70 μm filter (Corning Cat#352350), washed with cRPMI, and centrifuged at 1800 RPM for 10 min. Filtered brain homogenate was then resuspended with 20 mL of 40% Percoll (Cytiva Cat#17-0891-02) and centrifuged at 650 g for 25 min. Myelin was removed via aspiration of the upper layer. Brain samples were then resuspended in cRPMI. Spleens were mechanically homogenized and passed through a 40 μm filter (Corning Cat#352340), then washed with cRPMI and centrifuged at 1500 RPM for 5 min. Samples were resuspended in 1 mL of RBC lysis buffer (0.16 M NH4Cl) for 2 min. Cells were washed with cRPMI and centrifuged at 1500 RPM for 5 min and resuspended in cRPMI. For intracellular cytokine staining, cells were resuspended in 200 mL cRPMI with 20 mg/mL Brefeldin A (Selleckchem Cat#S7046) or a combination of 20 mg/mL Brefeldin A, 200 ng/mL Phorbol 12-Myristate 13-Acetate (PMA) (Sigma Aldrich Cat#P1585), and 1 mg/mL Ionomycin (Sigma Aldrich Cat#I0634) for 5 hours at 37° C. Cells suspensions were enumerated in a 1:10 dilution of 0.4% trypan blue solution (Sigma-Aldrich Cat#T8154) and manually counted on a hemocytometer (Hausser Scientific Cat#3110) using a DM 2000 LED brightfield microscope. Brains collected for cell lysate cytokine quantification by ELISA were placed into digestion buffer [HBSS with calcium and magnesium (ThermoScientific Cat# 14025092), 50 U/mL DNase, 4U/mL Papain (Worthington Biochemical Cat#LS003124)]. Brains were passed through an 18G needle and incubated for 15 min at 37° C; this was repeated three times over a 45 min incubation period. Post digestion, brain homogenate was passed through a 70 μm filter and washed with microglia growth media (MGM) [DMEM/F12 (Gibco Cat#11320-033), 10% FBS, 1% penicillin/streptomycin], and centrifuged at 1500 rpm for 5 min. Myelin was removed via Percoll gradient as previously described. Cells were washed with 5 mL of MGM and centrifuged at 1500 rpm for 5 min. Cells were resuspended in MGM and enumerated as previously described. 250,000 cells were plated per well into a 96-well plate in a total volume of 200 μL of MGM. Samples were incubated overnight at 37° C. To measure maximal cytokine levels, cells were treated with Triton X-100 (Sigma-Aldrich Cat#028SK001) (final concentration 0.1%) 30 minutes before collection. To collect supernatant, the plate was centrifuged at 1500 RPM for 2 min, and supernatant was transferred to a new 96-well plate and stored at -20° C.
Flow cytometry
Single cell suspensions were plated into a 96-well plate and centrifuged at 2000 RPM for 2 min. Cells were resuspended in 50 mL Fc Block: FACS buffer [(1X PBS, 0.2% bovine serum albumin (BSA) (Bioworld Cat#9048-46-8), and 2 mM EDTA (Invitrogen Cat#AM9260G)] with 0.1 μg/mL 2.4G2 antibody (BioXCell, Cat#CUS-HB-197) and 0.1% rat gamma globulin (Jackson Immunoresearch Cat#012-000-002) and incubated for 10 minutes at room temperature. Without washing off the Fc block, 50 mL FACS buffer containing antibodies for surface markers and fixable live/dead viability dye were added to the cells. Cells were incubated for 30 min at 4° C and then washed twice with 50 mL FACS buffer. Cells were fixed with fixation/permeabilization solution (eBioscience Cat#00-5123-43 and Cat#00-5223-56) for 20 min at room temperature or at 4° C overnight. For intracellular staining, cells were then washed twice with 50 mL 1X permeabilization buffer (eBioscience Cat#00-8333-56) and stained for intracellular markers in 1X permeabilization buffer for 30 min at 4° C. Finally, cells were resuspended in 200 mL FACS buffer and acquired using a 3 or 5 laser Cytek Aurora Flow Cytometry System. Data was analyzed using FlowJo software V10.10.0. The Fixable Viability Dye eFluor 780 (ThermoScientific Cat#50-112-9035) or eFluor 506 (ThermoScientific Cat#65-0866-18) was used at a dilution of 1:800. The following antibodies were used at a dilution of 1:200: CD45-AF700 (BioLegend Cat#103128), CD11b-PerCP Cy5.5 (ThermoScientific Cat#45-0112-80), CD11b-APC-eFluor 780 (ThermoScientific Cat#47-0112-82), Ly6G-BV711 (BioLegend Cat#127643), iNOS-APC (ThermoScientific Cat#17-5920-82), MHCII-Super Bright 780 (Fisher Scientific Cat#78-5321-82), MHCII-PE Cy5 (Fisher Scientific Cat#15-5322-81), CD11c-eFluor 506 (ThermoScientific Cat#69-0114-80), TCRb-APC (ThermoScientific Cat#17-5961-81), CD3e-FITC (ThermoScientific Cat#11-0031-85), CD3e-PE Cy7 (ThermoScientific Cat#25-0031-81), CD4-BV650 (Fisher Scientific Cat#563232), CD8-BV421 (Fisher Scientific Cat#563898), Foxp3-eFlour 450 (ThermoScientific Cat#48-5773-82), CD44-PE-eFlour 610 (ThermoScientific Cat#61-0441-82), CD62L-NovaFluor™ Blue 660-40S (ThermoScientific Cat# M006T02B07-A), IFNg-PerCP Cy5.5 (ThermoScientific Cat#45-7311-82), TNFa-PE (ThermoScientific Cat#12-7321-81), TNFa-AF488 (ThermoScientific Cat#53-7321-82), NK1.1-FITC (ThermoScientific Cat#11-0031-85), CD19-FITC (ThermoScientific Cat#11-0193-82), CD19-BV711 (Fisher Scientific Cat#563157), B220-FITC (ThermoScientific Cat#53-0452-82), B220-PE Cy5 (Fisher Scientific Cat#553091), IL-12p40-APC (BioLegend Cat#505205), CD64-PE Cy7 (BioLegend Cat#139314), NK1.1-Super Bright 780 (ThermoScientific Cat#78-5941-82), Tbet-PE Cy7 (ThermoScientific Cat#25-5825-80), Eomes-eFluor 450 (ThermoScientific Cat#48-4875-82). Ly6C-PE (ThermoScientific Cat#12-5932-82) was used at a dilution of 1:400.
Flow cytometry gating strategy
Peritoneum and spleen: Total IL-12+ cells (Size, singlets, live, IL-12+); IL-12+ dendritic cells (size, singlets, live, CD3/B220/CD19/NK1.1-, CD64-, CD11c+, MHCII+, IL-12+); NK cells (size, singlets, live, NK1.1+); NK cell cytokine (size, singlets, live, NK1.1+, IFNg or TNFa+); CD4 cells (size, singlets, live, TCRb+, CD4+); CD4 cell cytokine (size, singlets, live, TCRb+, CD4+, IFNg or TNFa+); CD8 cells (size, singlets, live, TCRb+, CD8+); CD8 cell cytokine (size, singlets, live, TCRb+, CD8+, IFNg or TNFa+); ILC1s (size, singlets, live, NK1.1+, CD127+, Tbet+); ILC1 cytokine (size, singlets, live, NK1.1+, CD127+, Tbet+, IFNg or TNFa+); myeloid TNFa (size, singlets, live, CD45+, CD11b+, TNFa+); neutrophils (size, singlets, live, CD45+, CD11b+, Ly6G+); infiltrating monocytes (size, singlets, live, CD45+, CD11b+, Ly6G-, Ly6Chi, MHCII+); iNOS producing inflammatory monocytes (size, singlets, live, CD45+, CD11b+, Ly6G-, Ly6Chi, iNOS+); NKT cells (size, singlets, live, NK1.1+, TCRb+); NKT cell cytokine (size, singlets, live, NK1.1+, TCRb+, IFNg or TNFa+)
Brain: neutrophils (size, singlets, live, CD45hi, CD11b+, Ly6G+); infiltrating monocytes (size, singlets, live, CD45hi, CD11b+, Ly6G-, Ly6Chi, MHCII+); iNOS producing inflammatory monocytes (size, singlets, live, CD45hi, CD11b+, Ly6G-, Ly6Chi, iNOS+); CD4 cells (size, singlets, live, TCRb+, CD4+); CD4 cell cytokine (size, singlets, live, TCRb+, CD4+, IFNg or TNFa+); CD8 cells (size, singlets, live, TCRb+, CD8+); CD8 cell cytokine (size, singlets, live, TCRb+, CD8+, IFNg or TNFa+).
ELISA
Serum, peritoneal exudate fluid, and cell lysate cytokine levels were detected according to the manufacturer’s instructions using Quantikine ELISA [Mouse IL-12 p40 allele specific (R&D Systems Cat#M1240)] and DuoSet ELISA [Mouse IFN-gamma (R&D Systems Cat# DY485), Mouse TNF-alpha (R&D Systems Cat#DY410-05), Mouse IL-1 alpha/IL-1F1 (R&D Systems Cat #DY400-05), Mouse IL-18 (R&D Systems Cat# DY7625-05)] with the DuoSet Ancillary Reagent Kit 2 (R&D Systems Cat# DY008B).
Parasite burden assessments
Parasite burden was measured by real-time PCR of genomic DNA (gDNA). gDNA was isolated from mouse PECs and brain, with brain tissue first being homogenized in PBS using the Omni TH tissue homogenizer (Omni International), using the Isolate II Genomic DNA Kit (Bioline Cat#BIO-52067). The T. gondii 529 bp repeat region was amplified using the SensiFAST Probe No-ROX Kit (Bioline Cat#BIO-86005) and CFX384 Real-Time System (Bio-Rad) as previously described.61 500 ng of gDNA was loaded into each reaction. The number of T. gondii genomes per mg of tissue DNA was quantified by a standard curve ranging from 3 to 300,000 genome copies. To measure brain parasite burden by cyst counts, whole brains were passed through an 18G then 22G needle to mechanically homogenize the tissue. Cysts were enumerated as described in the “Parasite and Infection” methods section.
RT-qPCR
To measure gene expression, PECs were homogenized directly in Trizol (Fisher Scientific Cat#15-596-026) while brains samples were loaded into tubes (Sarstedt, Cat# 72.693.005) containing Trizol reagent and zirconia/silica beads (Biospec Cat#11079110z) and homogenized for 30 seconds with a Mini-bead beater (Biospec Cat# 607) machine. RNA was extracted according to the manufacturer’s protocol. High-Capacity Reverse Transcription Kit (Applied Biosystems Cat# 4374967) was used to generate cDNA. Quantitative PCR was performed using 2X Taq-based Master Mix (Bioline Cat#21105) and Taq Man gene expression assays (ThermoScientific Cat#4331182). Samples were run on a CFX384 Real-Time System thermocycler (Bio-Rad Laboratories). Genes were normalized to murine Hprt and relative expression was calculated using the 2 (-ΔΔCT) method.62 The following ThermoFisher mouse gene probes were used: Hprt (Mm00446968_m1), Cxcl1 (Mm00445235_m1), Cxcl2 (Mm00436450_m1), Ccl2 (Mm00441242_m1), Ccr2 (Mm04207877_m1), Zbp1 (Mm01247052_m1) Nos2 (Mm00440502_m1), Ifng (Mm01168134_m1), Tnf (Mm00443258_m1), Il1a (Mm00439620_m1), Il1b (Mm00434228_m1), Icam1 (Mm00516023_m1), Vcam1 (Mm01320970_m1).
Multiplexed Error-Robust Fluorescence in Situ Hybridization (MERFISH)
To measure spatially resolved RNA transcripts in individually segmented nuclei in whole brain slices a 342 gene panel was created, including housekeeping genes, genes to differentiate cell types, and genes related to inflammation and cell death. C57BL/6 mice were injected i.p. with saline or Me49 and sacrificed 28 days post-injection. Dissected brains were fresh frozen (embedded in OCT and frozen in isopentane chilled with liquid nitrogen), then sectioned at 10 mm thickness (Leica CM1950) directly onto MERSCOPE slides (Vizgen). MERSCOPETM User Guide for Fresh and Fixed Frozen Tissue Sample Preparation Rev D, with amendments made based on MERSCOPE Quick Guide Modified Fixation for Fresh & Fixed Frozen Sample Preparation Rev A and MERSCOPE Technical Note Improving Tissue Adherence Rev A were used to prepare slides. The Vizgen Post-Processing Tool (v1.1.2) was used for cell segmentation and configured to use the Cellpose cyto2 model. DAPI+ nuclear signal from the third z-plane was used for cylindrical segmentation. Segmentation output files generated by VPT were imported into a Python 3 environment using Squidpy (v1.2.2) to construct an AnnData (v0.10.4) cell-by-gene expression matrix. To filter out low-quality or false cell profiles, nuclei were only retained if they contained more than 20 total transcripts. Additionally, nuclei total transcript counts, number of detected genes, and cell volume had to fall within the following thresholds: total transcript counts and detected genes greater than 20 and below the 99th percentile, nuclear volume within the 1st to 99th percentiles. Samples were integrated into a shared latent space using scVI-tools (v1.0.4). High-quality cells were then annotated through Leiden clustering and differential expression of canonical cell type marker genes analysis using the Wilcoxon rank-sum test in Scanpy (v1.9.6). Saline injected (“naïve”): n=55,399 cells, 32,247 transcripts per field of view (FOV); Me49 injected (“28 dpi”): n=58,479 cells, 29,758 transcripts per FOV. Vizgen MERSCOPE Visualizer software was used to produce figures.
Statistical analysis
Experiments with only one experimental replicate were analyzed using GraphPad Prism 9, an unpaired t-test, or a one-way ANOVA. Experiments with multiple replicates were analyzed in R using a randomized block ANOVA and Least-Squares Means paired with a Tukey post-hoc analysis to adjust p-values for multiple comparisons. This analysis accounts for the biological variability between infections, with the experimental group modeled as a fixed effect and the experimental day modeled as a random effect.63 All data was graphed in GraphPad Prism 9. Outliers were identified and removed using the ROUTs method with a Q value of 1. p values are indicated, with *p<0.05, **p<0.01, ***p<0.001.
