Immunopeptidomics:Article Title: Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population
Article Snippet: .. rabbit anti-SARS-CoV-2 nucleocapsid protein (5ug/ml) Novus Biologicals Cat# NB100-56576 rabbit anti-human CD31 (2ug/ml) Novus Biologicals Cat# NB100-2284 rabbit anti-human SP-C (4.17ug/ml) Novus Biologicals Cat# NBP1-60117 mouse anti-human CD68 (5ug/ml) Agilent Cat# M0876 rabbit anti-human KRT8 (2.5ug/ml) Abcam Cat# ab59400 anti-human Smooth muscle actin (SMA) (clone 1A4) Bio-Rad Cat# MCA5781GA anti-humanCD68 (clone KP1) Thermo Cat# MA5-13324 anti-human CD235ab (clone HIR2) BioLegend Cat# 306615 anti-human Pan-cytokeratin (PanCK) (clone AE-1/AE-3) Biolegend Cat# 914204 anti-human CD38 (clone EPR4106) Standard Biotools Cat# 3141018D anti-human MHC I (clone EMR8-5) Abcam Cat# ab70328 anti-human Vimentin (clone RV202) Standard Biotools Cat# 3143029D anti-human CD14 (clone D7A2T) Cell Signalling Cat# 56082BF anti-human ICAM1 (clone EP1442Y) Abcam Cat# ab271852 anti-human CD16 (clone SP175) Abcam Cat# ab243925100ug anti-human iNOS (clone SP126) abcam Cat# ab239990 anti-human CD66b (G10F5) Novus Cat# g10f5_nb10077808 anti-human CD11b (EP1345Y) Abcam Cat# ab5247 anti-human CD44 (IM7) BioLegend Cat# 103001 anti-human CD107a (H4A3) Standard Biotools Cat# 3151021D anti-human CD45 (CD45-2B11) eBioscience Cat# 14-9457-82 anti-human CD31 (JC/70A) Novus Cat# jc-70a_nb600562 anti-human CD11c (Polyclonal) Standard Biotools Cat# 3154025D anti-human Foxp3 (clone 236A/E7) Abcam Cat# ab20034 anti-human CD4 (clone EPR6855) Standard Biotools Cat# 3156033D anti-human SARS-Cov-2 (Polyclonal) Novus Cat# NB100-56576 anti-human Von Willebrand Factor (vWF) (Polyclonal) Dako Cat# A0082 anti-human Vista (clone D1L2G) Standard Biotools Cat# 3160025D anti-human CD20 (clone H1) Standard Biotools Cat# 3161029D anti-human CD8 (clone CD8/144B) eBioscience Cat# 14-0085-82 anti-human Iba1 (Polyclonal) WAKO Cat# 019-19741 anti-human Arginase 1 (clone D4E3M) Standard Biotools Cat# 3164027D anti-human Fibrinogen (EPR18145-84) Abcam Cat# ab227063 anti-human CD74 (clone LN2) Standard Biotools Cat# 3166025D anti-human Granzyme B (clone EPR20129-217) Standard Biotools Cat# 3167021D anti-human Collagen Type I (Polyclonal) Standard Biotools Cat# 3169023D anti-human CD3 (clone D7A6E) Cell Signalling Cat# 85061BF anti-human pERK1/2 [T202/Y204] (clone D13.14.4E) Standard Biotools Cat# 3171021D anti-human Cleaved Caspase 3 (clone 5A1E) Standard Biotools Cat# 3172023A anti-human CD45RO (clone UCHL1) Standard Biotools Cat# 3173016D anti-human MHC II (clone TAL1B5) Abcam Cat# ab176408 anti-human CD206 (clone E2L9N) Cell Signalling Cat# 91992 anti-human CD163 (clone EDHu-1) Bio-Rad Cat# MCA1853 .. Package name Reference (where applicable) URL R v4.3.0 https://www.cran.r-project.org Python v3.9.6 https://www.python.org RStudio software (v 2023.03.0+386; 2023) The R project for Statistical Computing https://www.rstudio.com/ and https://cran.r-project.org/ Ilastik v1.4.0 Berg et al., 2019 https://www.ilastik.org CellProfiler v4.2.4 https://cellprofiler.org FactoMineR v2.8 (R package) Sebastien Le, 2008 https://cran.r- project.org/web/packages/Fact oMineR/index.html ggplot2 v3.4.2 (R package) https://ggplot2.tidyverse.org factoextra v1.0.7 (R package) https://cran.r- project.org/web/packages/facto extra/index.html corrplot v0.92 (R package) https://cran.r- project.org/web/packages/corr plot/vignettes/corrplot- intro.html missMDA v1.18 (R package) Josse and Husson, 2016 https://cran.r- project.org/web/packages/miss MDA/index.html tidymodels v1.0.0 (R package) https://www.tidymodels.org cytomapper v1.9.2 (R package) Nils Eling, 2020 https://github.com/Bodenmiller Group/cytomapper miloR v1.4.0 (R package) (Dann et al., 2022) https://marionilab.github.io/mil oR Giotto v3.3.0 (R package) Dries et al., 2021 https://giottosuite.readthedocs. io/en/latest/ ImcSegmentationPipeline (Python package) Vito RT Zanotelli, 2022 https://github.com/Bodenmiller Group/ImcSegmentationPipelin e IMC-Denoise (Python package) Lu et al., 2023 https://github.com/PENGLU- WashU/IMC_Denoise DeepCell (Python package) Greenwald et al., 2022 https://github.com/vanvalenlab /deepcell-tf Scanpy (Single-Cell Analysis in Python) v1.9.1 (Python package) (Wolf et al., 2018 https://github.com/scverse/sca npy umap-learn v0.5.3 (Python package) (McInnes, 2018 https://github.com/lmcinnes/u map Astir (ASsignmenT of sIngle-cell pRoteomics) v0.1.4 (Python package) Geuenich et al., 2021 https://github.com/camlab- bioml/astir Squidpy (Spatial Quantification of Molecular Data in Python) v1.2.2 (Python package) Palla et al., 2022 https://squidpy.readthedocs.io/ en/stable/ Athena (Analysis of Tumor HEterogeNeity from spAtial omics measurements) v 0.1.3 (Python package) (Martinelli and Rapsomaniki, 2022 https://ai4scr.github.io/ATHENA /index.html SpOOx (Spatial Omics Oxford Pipeline) (Python package) (Praveen Weeratunga, 2022 https://github.com/Taylor-CCB- Group/SpOOx Supplemental Figure 1 | Histological characteristics of lung pathology in patients with SARS CoV-2 infection A B C D E F * * * * * * * * * * * * ** * * * * Supplemental data, Fig. 1 Supplemental Figure 2 | Top cluster markers characterising immune and stromal cell populations in the lung in the Malawi cohort Supplemental Figure 3 | Characterisation of cell populations in the nasal and peripheral blood tissue compartments in the Malawi cohort.
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