other:Article Title: Klebsiella pneumoniae hijacks the Toll-IL-1R protein SARM1 in a type I IFN-dependent manner to antagonize host immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-IL-1b R&D Systems Cat# AF-401-NA, RRID:AB_416684 anti-caspase-1 Cell Signaling Cat# 24232, RRID:AB_2890194 anti-AIM2 Santa Cruz Cat# sc-515895; RRID:AB_2922903 anti-NLRP3 Cell Signaling Cat# 15101; RRID:AB_2922902 anti-Gasdermin-D Cell Signaling Cat# 93709; RRID:AB_2800210 anti-Viperin Novus Biologicals Cat# NBP2-03971; RRID:AB_2922904 anti-ISG15 Cell Signaling Cat# 2743: AB_485250 anti-phospho-STAT3 Cell Signaling Cat# 9145; RRID:AB_2799407 anti-IkBa Cell Signaling Cat# 4814; RRID:AB_2797687 anti-phospho-IkBa Cell Signaling Cat# 9246; RRID:AB_2922905 anti-phospho-AKT1/2/3 Santa Cruz Cat# sc-33437; RRID:AB_2922906 anti-phospho-IKKa/b Cell Signaling Cat# 2697; RRID:AB_2922907 anti-phospho-IRF3 Cell Signaling Cat# 4947; RRID:AB_823547 anti-phospho-p-TBK-1/NAK Cell Signaling Cat# 5483; RRID:AB_2922908 anti-phospho-JNK Cell Signaling Cat# 9251S; RRID:AB_331659 anti-phospho-ERK Cell Signaling Cat# 9101; RRID:AB_331772 anti-phospho-p38 Cell Signaling Cat# 4511; RRID:AB_2797648 anti-Flag M2 Sigma-Aldrich Cat# F3165; RRID:AB_2922909 anti-HA Santa Cruz Cat# sc-805; RRID:AB_2922910 anti a-tubulin Sigma-Aldrich Cat# T9026; RRID:AB_2922911 anti-b-actin Santa Cruz Cat# sc-130065; RRID:AB_2922912 anti-ASC Santa Cruz Cat# sc-22514R; RRID:AB_2922913 anti-Lamp1 Santa Cruz Cat# sc-19992; RRID:AB_2922914 anti-Rab14 Santa Cruz Cat# sc-271401; RRID:AB_2922915 Ly6G Fluidigm Cat# 3141008B; RRID:AB_2814678 SIRPa BD Biosciences Cat# 552371; RRID: AB_394371 B220 Fluidigm Cat# 3144011B; RRID:AB_2811239 CD4 Fluidigm Cat# 3145002B; RRID:AB_2687832 F4/80 Fluidigm Cat# 3146008B; RRID:AB_2895117 CD45 Fluidigm Cat# 3147003C; RRID:AB_2811243 CD11b Fluidigm Cat# 3148003C; RRID:AB_2922916 CD19 Fluidigm Cat# 3149002B; RRID:AB_2814679 CD24 Fluidigm Cat# 3150009B; RRID:AB_2922917 CD25 Fluidigm Cat# 151007B; RRID:AB_2687835 CD3e Fluidigm Cat# 3152004B; RRID:AB_2687836 PD-L1 Fluidigm Cat# 3153016B; RRID:AB_2687837 CD103 BioLegend Cat# 121402; RRID:AB_535945 CD90.2 Fluidigm Cat# 3156006B; RRID:AB_2801433 IL-10 Fluidigm Cat# 3158002B; RRID:AB_2922918 TCRgd Fluidigm Cat# 3159012B; RRID:AB_2922919 CD62L Fluidigm Cat# 3160008C; RRID:AB_2885021 iNOS Fluidigm Cat# 3161011B; RRID:AB_2922920 Ly6C Fluidigmn Cat# 3162014B; RRID:AB_2922921 (Continued on next page) Cell Reports 40, 111167, August 9, 2022 e1
Virus:Article Title: Anatomical, subset, and HIV-dependent expression of viral sensors and restriction factors.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD57 Biolegend Cat#359602; RRID:AB_2562403 HLADR Thermo Fisher Scientific Cat#Q22158; RRID:AB_2556514 CD25 BD Biosciences Cat#555430; RRID:AB_395824 CD19 Standard BioTools Cat#3142001B; RRID:AB_3661857 IFI16 Santa Cruz Biotechnology Cat#sc-8023; RRID:AB_627775 CCR5 Standard BioTools Cat#3144007A; RRID:AB_2892770 IFITM1 Proteintech Cat#60074-1-Ig; RRID:AB_2233405 CD8 Standard BioTools Cat#3146001B; RRID:AB_3661846 cGAS Cell Signaling Technology Cat#79978S; RRID:AB_2905508 IFIT3 Novus Cat#NBP2-71006; RRID:AB_3094693 AIM2 Santa Cruz Biotechnology Cat#sc-293174; RRID:AB_3665129 HSA (CD24) Standard BioTools Cat3150009B; RRID:AB_2916042 LAG3 Standard BioTools Cat#3150030B; RRID:AB_3661851 pSTING Cell Signaling Technology Cat#40818; RRID:AB_2799187 SLFN11 Santa Cruz Biotechnology Cat#sc-374339; RRID:AB_10989536 MX2 Santa Cruz Biotechnology Cat#sc-271527; RRID:AB_10649506 IFIT1 Novus Cat#NBP2-71005; RRID:AB_3363102 pIRF3 Cell Signaling Technology Cat#29047; RRID:AB_2773013 SAMHD1 Proteintech Cat#12586-1-AP; RRID:AB_2183496 TRIM28 R and D Systems Cat#MAB7785; RRID:AB_3096992 PAF1 Santa Cruz Biotechnology Cat#sc-514491; RRID:AB_3665128 CCR7 Standard BioTools Cat#3159003A; RRID:AB_2938859 MX1 Cell Signaling Technology Cat#62815; RRID:AB_3665127 CD45RO Biolegend Cat#304239; RRID:AB_2563752 CD69 Standard BioTools Cat#3162001B; RRID:AB_3096016 TLR9 Novus Cat#NBP2-24729; RRID:AB_3272891 CXCR5 Standard BioTools Cat#3164029B; RRID:AB_3665126 pSAMHD1 Sigma-Aldrich Cat#MABF934; RRID:AB_3665125 PQBP1 Santa Cruz Biotechnology Cat#sc-376039; RRID:AB_10989350 CD27 Standard BioTools Cat#3167002B; RRID:AB_3094744 PD1 BD Biosciences Cat#562138; RRID:AB_10897007 CD45RA Standard BioTools Cat#3169008B; RRID:AB_3665124 CD3 Standard BioTools Cat#3170001B; RRID:AB_2811085 RIGI Novus Cat#NBP2-61849; RRID:AB_3351257 CD38 Standard BioTools Cat#3172007B; RRID:AB_2756288 BRD4 Abcam Cat#ab182446; RRID:AB_3665123 CD4 Standard BioTools Cat#3174004B; RRID:AB_3661864 CD14 Biolegend Cat#301843; RRID:AB_2562813 CD127 Standard BioTools Cat#3176004B; RRID:AB_3665122 TIGIT Standard BioTools Cat#3209013B; RRID:AB_2905649 Bacterial and virus strains HIV-F4.HSA (NL-HSA.6ATRi-C.109FPB4.ecto) Cavrois et al.34 N/A HIV-F4.HSA virions containing BlaM-Vpr Cavrois et al.34,67 N/A (Continued on next page) 16 Cell Reports 44, 115202, January 28, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism (Version 10.2.0) http://www.graphpad.com/ RRID:SCR_002798 RStudio (2022.07.2 + 576 "Spotted Wakerobin" Release) https://rstudio.com/ RRID:SCR_000432 R Project for Statistical Computing (Version 4.2.1) http://www.r-project.org/ RRID:SCR_001905 CUHIMSR/CytofBatchAdjust Schuyler et al.95; https://github.com/ CUHIMSR/CytofBatchAdjust N/A ggplot2 https://cran.r-project.org/web/ packages/ggplot2/index.html RRID:SCR_014601 Rtsne https://github.com/jkrijthe/Rtsne RRID:SCR_016342 Seurat Hao et al.96; https://satijalab.org/ seurat/get_started.html RRID:SCR_016341 Harmony Korsunsky et al.97; https://github.com/ immunogenomics/harmony RRID:SCR_022206 RandomForest Package in R Breiman98; https://cran.r-project. org/web/packages/randomForest/ RRID:SCR_015718 lme4 Bates et al.99; https://cran.r-project. org/web/packages/lme4/index.html RRID:SCR_015654 emmeans https://CRAN.R-project.org/ package=emmeans RRID:SCR_018734
Immunopeptidomics:Article Title: High-resolution phenotyping of early acute rejection reveals a conserved alloimmune signature.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Gr1 (RB6-8C5); Clone preferentially binds Ly6G Fluidigm Cat#3141005B; Lot#1201813 CD11c (N418) Fluidigm Cat#3142003B; Lot#1201819 GITR (DTA1) Fluidigm Cat#3143019B; Lot#2171502 MHCI (28-14-8) Fluidigm Cat#3144016B; Lot#0151802 CD69 (H1.2F3) Fluidigm Cat#3145005B; Lot#3511606 CD5 (53-7.3) Fluidigm Cat#3146012B; Lot#2041519 CD45 (30-F11) Fluidigm Cat#3147003B; Lot#3181713 CD11b (M1/70); Alt. name: Mac-1 Fluidigm Cat#3148003B; Lot#1621803 CD19 (6D5) Fluidigm Cat#3149002B; Lot#0581828 CD24 (M1/69) Fluidigm Cat3150009B; Lot#0901508 CD25 (3C7) Fluidigm Cat#3151007B; Lot#3511605 CD3ε (145 2X11) Fluidigm Cat#3152004B; Lot#2601606 CD8a (53 6.7) Fluidigm Cat#3153012B; Lot#0101806 CTLA4 (UC10-4B9); Alt. name: CD152 Fluidigm Cat#3154008B; Lot#1841809 TCRgd (UC7-13D5) Biolegend Cat#107502 CCR6 (29-2L17); Alt. name: CD196 Fluidigm Cat#3156016A; Lot#0581825 CD80 (16-10A1); Alt. name: B7-1 Biolegend Cat#104702 FOXP3 (FJK-16 s) Fluidigm Cat#3158003A; Lot#0691401 F4/80 (BM8) Fluidigm Cat#3159009B; Lot#0541707 CD62L (MEL-14) Fluidigm Cat#3160008B; Lot#2631805 Ly6C (HK1.4) Fluidigm Cat#3162014B; Lot#2341706 CCR7 (4B12); Alt. name: CD197 Fluidigm Cat#3164013A; Lot#0901709 NK1.1 (PK136) Fluidigm Cat#3165018B; Lot#0101808 CD27 (LG.3A10) Biolegend Cat#124202 NKp46 (29A1.4); Alt. name: CD335 Fluidigm Cat#3167008B; Lot#1501808 CD21 (7G6) Fluidigm Cat#3168010B; Lot#2371409 TCRb (H57 597) Fluidigm Cat#3169002B; Lot#0761712 CD40L (MR1); Alt. name: CD154 Fluidigm Cat#3170011B; Lot#2041508 CD44 (IM7) Fluidigm Cat#3171003B; Lot#3421608 CD4 (RM4-5) Fluidigm Cat#3172003B; Lot#1201808 Granzyme B (GB11) Fluidigm Cat#3173006B; Lot#1511802 LAG3 (C9B7W) Fluidigm Cat#3174019B; Lot#1201814 CD127 (A7R34); Alt. name: IL7Ra Fluidigm Cat#3175006B; Lot#0101807 B220 (RA3-6B2); Alt. name: CD45R Fluidigm Cat#3176002B; Lot#0321704 MHCII I-A/I-E (M5/114.15.2); Binds both donor and recipient MHC Fluidigm Cat#3209006B; Lot#2851707 Fc Block: TruStain FcX (anti-mouse CD16/32) Antibody Biolegend Cat#101320 Critical commercial assays Dead cell removal kit StemCell Cat#17899 40 micron nylon mesh Fisher Cat#352340 Cisplatin Fluidigm Cat#201195 Cell staining buffer Fluidigm Cat#201068 Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 (Continued on next page) e1 Cell Reports 34, 108806, March 2, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fix I buffer Fluidigm Cat#201065 Perm-S buffer Fluidigm Cat#201066 Fix and perm buffer Fluidigm Cat#201067 DNA intercalator Fluidigm Cat#201192a 35 micron cell strainer Fisher Cat#08-771-23 Experimental models: organisms/strains Mouse: C57BL/6 (H-2Kb) The Jackson Laboratory JAX: 000664 Mouse: BALB/c (H-2Kd) The Jackson Laboratory JAX: 000651 Software and algorithms Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa FlowSOM (v1.18.0) Van Gassen et al., 2020 https://bioconductor.org/packages/release/bioc/ html/FlowSOM.html ConsensusClusterPlus (v1.50.0) Wilkerson and Hayes, 2010 https://bioconductor.org/packages/release/bioc/ html/ConsensusClusterPlus.html UMAP; v0.3.2.1 Becht et al., 2018 https://github.com/lmcinnes/umap Rtsne; v0.15 van der Maaten and Hinton, 2008 https://github.com/jkrijthe/Rtsne
Blocking Assay:Article Title: High-resolution phenotyping of early acute rejection reveals a conserved alloimmune signature.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Gr1 (RB6-8C5); Clone preferentially binds Ly6G Fluidigm Cat#3141005B; Lot#1201813 CD11c (N418) Fluidigm Cat#3142003B; Lot#1201819 GITR (DTA1) Fluidigm Cat#3143019B; Lot#2171502 MHCI (28-14-8) Fluidigm Cat#3144016B; Lot#0151802 CD69 (H1.2F3) Fluidigm Cat#3145005B; Lot#3511606 CD5 (53-7.3) Fluidigm Cat#3146012B; Lot#2041519 CD45 (30-F11) Fluidigm Cat#3147003B; Lot#3181713 CD11b (M1/70); Alt. name: Mac-1 Fluidigm Cat#3148003B; Lot#1621803 CD19 (6D5) Fluidigm Cat#3149002B; Lot#0581828 CD24 (M1/69) Fluidigm Cat3150009B; Lot#0901508 CD25 (3C7) Fluidigm Cat#3151007B; Lot#3511605 CD3ε (145 2X11) Fluidigm Cat#3152004B; Lot#2601606 CD8a (53 6.7) Fluidigm Cat#3153012B; Lot#0101806 CTLA4 (UC10-4B9); Alt. name: CD152 Fluidigm Cat#3154008B; Lot#1841809 TCRgd (UC7-13D5) Biolegend Cat#107502 CCR6 (29-2L17); Alt. name: CD196 Fluidigm Cat#3156016A; Lot#0581825 CD80 (16-10A1); Alt. name: B7-1 Biolegend Cat#104702 FOXP3 (FJK-16 s) Fluidigm Cat#3158003A; Lot#0691401 F4/80 (BM8) Fluidigm Cat#3159009B; Lot#0541707 CD62L (MEL-14) Fluidigm Cat#3160008B; Lot#2631805 Ly6C (HK1.4) Fluidigm Cat#3162014B; Lot#2341706 CCR7 (4B12); Alt. name: CD197 Fluidigm Cat#3164013A; Lot#0901709 NK1.1 (PK136) Fluidigm Cat#3165018B; Lot#0101808 CD27 (LG.3A10) Biolegend Cat#124202 NKp46 (29A1.4); Alt. name: CD335 Fluidigm Cat#3167008B; Lot#1501808 CD21 (7G6) Fluidigm Cat#3168010B; Lot#2371409 TCRb (H57 597) Fluidigm Cat#3169002B; Lot#0761712 CD40L (MR1); Alt. name: CD154 Fluidigm Cat#3170011B; Lot#2041508 CD44 (IM7) Fluidigm Cat#3171003B; Lot#3421608 CD4 (RM4-5) Fluidigm Cat#3172003B; Lot#1201808 Granzyme B (GB11) Fluidigm Cat#3173006B; Lot#1511802 LAG3 (C9B7W) Fluidigm Cat#3174019B; Lot#1201814 CD127 (A7R34); Alt. name: IL7Ra Fluidigm Cat#3175006B; Lot#0101807 B220 (RA3-6B2); Alt. name: CD45R Fluidigm Cat#3176002B; Lot#0321704 MHCII I-A/I-E (M5/114.15.2); Binds both donor and recipient MHC Fluidigm Cat#3209006B; Lot#2851707 Fc Block: TruStain FcX (anti-mouse CD16/32) Antibody Biolegend Cat#101320 Critical commercial assays Dead cell removal kit StemCell Cat#17899 40 micron nylon mesh Fisher Cat#352340 Cisplatin Fluidigm Cat#201195 Cell staining buffer Fluidigm Cat#201068 Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 (Continued on next page) e1 Cell Reports 34, 108806, March 2, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fix I buffer Fluidigm Cat#201065 Perm-S buffer Fluidigm Cat#201066 Fix and perm buffer Fluidigm Cat#201067 DNA intercalator Fluidigm Cat#201192a 35 micron cell strainer Fisher Cat#08-771-23 Experimental models: organisms/strains Mouse: C57BL/6 (H-2Kb) The Jackson Laboratory JAX: 000664 Mouse: BALB/c (H-2Kd) The Jackson Laboratory JAX: 000651 Software and algorithms Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa FlowSOM (v1.18.0) Van Gassen et al., 2020 https://bioconductor.org/packages/release/bioc/ html/FlowSOM.html ConsensusClusterPlus (v1.50.0) Wilkerson and Hayes, 2010 https://bioconductor.org/packages/release/bioc/ html/ConsensusClusterPlus.html UMAP; v0.3.2.1 Becht et al., 2018 https://github.com/lmcinnes/umap Rtsne; v0.15 van der Maaten and Hinton, 2008 https://github.com/jkrijthe/Rtsne
Staining:Article Title: High-resolution phenotyping of early acute rejection reveals a conserved alloimmune signature.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Gr1 (RB6-8C5); Clone preferentially binds Ly6G Fluidigm Cat#3141005B; Lot#1201813 CD11c (N418) Fluidigm Cat#3142003B; Lot#1201819 GITR (DTA1) Fluidigm Cat#3143019B; Lot#2171502 MHCI (28-14-8) Fluidigm Cat#3144016B; Lot#0151802 CD69 (H1.2F3) Fluidigm Cat#3145005B; Lot#3511606 CD5 (53-7.3) Fluidigm Cat#3146012B; Lot#2041519 CD45 (30-F11) Fluidigm Cat#3147003B; Lot#3181713 CD11b (M1/70); Alt. name: Mac-1 Fluidigm Cat#3148003B; Lot#1621803 CD19 (6D5) Fluidigm Cat#3149002B; Lot#0581828 CD24 (M1/69) Fluidigm Cat3150009B; Lot#0901508 CD25 (3C7) Fluidigm Cat#3151007B; Lot#3511605 CD3ε (145 2X11) Fluidigm Cat#3152004B; Lot#2601606 CD8a (53 6.7) Fluidigm Cat#3153012B; Lot#0101806 CTLA4 (UC10-4B9); Alt. name: CD152 Fluidigm Cat#3154008B; Lot#1841809 TCRgd (UC7-13D5) Biolegend Cat#107502 CCR6 (29-2L17); Alt. name: CD196 Fluidigm Cat#3156016A; Lot#0581825 CD80 (16-10A1); Alt. name: B7-1 Biolegend Cat#104702 FOXP3 (FJK-16 s) Fluidigm Cat#3158003A; Lot#0691401 F4/80 (BM8) Fluidigm Cat#3159009B; Lot#0541707 CD62L (MEL-14) Fluidigm Cat#3160008B; Lot#2631805 Ly6C (HK1.4) Fluidigm Cat#3162014B; Lot#2341706 CCR7 (4B12); Alt. name: CD197 Fluidigm Cat#3164013A; Lot#0901709 NK1.1 (PK136) Fluidigm Cat#3165018B; Lot#0101808 CD27 (LG.3A10) Biolegend Cat#124202 NKp46 (29A1.4); Alt. name: CD335 Fluidigm Cat#3167008B; Lot#1501808 CD21 (7G6) Fluidigm Cat#3168010B; Lot#2371409 TCRb (H57 597) Fluidigm Cat#3169002B; Lot#0761712 CD40L (MR1); Alt. name: CD154 Fluidigm Cat#3170011B; Lot#2041508 CD44 (IM7) Fluidigm Cat#3171003B; Lot#3421608 CD4 (RM4-5) Fluidigm Cat#3172003B; Lot#1201808 Granzyme B (GB11) Fluidigm Cat#3173006B; Lot#1511802 LAG3 (C9B7W) Fluidigm Cat#3174019B; Lot#1201814 CD127 (A7R34); Alt. name: IL7Ra Fluidigm Cat#3175006B; Lot#0101807 B220 (RA3-6B2); Alt. name: CD45R Fluidigm Cat#3176002B; Lot#0321704 MHCII I-A/I-E (M5/114.15.2); Binds both donor and recipient MHC Fluidigm Cat#3209006B; Lot#2851707 Fc Block: TruStain FcX (anti-mouse CD16/32) Antibody Biolegend Cat#101320 Critical commercial assays Dead cell removal kit StemCell Cat#17899 40 micron nylon mesh Fisher Cat#352340 Cisplatin Fluidigm Cat#201195 Cell staining buffer Fluidigm Cat#201068 Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat#201060 (Continued on next page) e1 Cell Reports 34, 108806, March 2, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fix I buffer Fluidigm Cat#201065 Perm-S buffer Fluidigm Cat#201066 Fix and perm buffer Fluidigm Cat#201067 DNA intercalator Fluidigm Cat#201192a 35 micron cell strainer Fisher Cat#08-771-23 Experimental models: organisms/strains Mouse: C57BL/6 (H-2Kb) The Jackson Laboratory JAX: 000664 Mouse: BALB/c (H-2Kd) The Jackson Laboratory JAX: 000651 Software and algorithms Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa FlowSOM (v1.18.0) Van Gassen et al., 2020 https://bioconductor.org/packages/release/bioc/ html/FlowSOM.html ConsensusClusterPlus (v1.50.0) Wilkerson and Hayes, 2010 https://bioconductor.org/packages/release/bioc/ html/ConsensusClusterPlus.html UMAP; v0.3.2.1 Becht et al., 2018 https://github.com/lmcinnes/umap Rtsne; v0.15 van der Maaten and Hinton, 2008 https://github.com/jkrijthe/Rtsne
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