Journal: Nature immunology

Article Title: Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

doi: 10.1038/s41590-018-0276-y

Figure Lengend Snippet: a, Pdgfa expression in lung scRNA-seq macrophage clusters and by bulk RNA-seq of SiglecF + CD11c + lung macrophages after bleomycin injury. Mean is marked. Wald test 2-sided p-value is presented (for the lung scRNA-seq data, n=3 biologically independent mice for bleomycin-injured and n=6 biologically independent mice for healthy control; for the bulk RNA-seq data, n=2 biologically independent mice for baseline, n=3 biologically independent mice for all other conditions). b, Lung immunofluorescence at baseline (bottom) and 14 days after injury (top) in tamoxifen-induced Cx3cr1 -CreERT2 / Rosa26 loxp STOP loxp -TdTomato mice (representative images are shown; quantitation is for the 14-day time point in n=3 biologically independent mice, 5 images per mouse). Scale bar, 50 μm. c, 3T3 fibroblast gap closure in response to conditioned media (CM) from lung macrophages sorted by MHCII expression, with and without Pdgf-aa blocking antibody (Ab; n=8 biologically independent mice total, each point a separate assay). d , EDU quantitation in 3T3 fibroblasts co-cultured with TdTomato + cells sorted from tamoxifen-induced Cx3cr1 -CreERT2 / Rosa26-loxp-STOP-loxp-TdTomato mice 14 days after injury. Mean is marked (n=3 biologically independent co-cultures). e , t-SNE of SingleR-annotated fibroblasts from the lung scRNA-seq dataset showing intensity of cell cycle signature (n=3 biologically independent mice for bleomycin, n=6 biologically independent mice for control). Box plot center lines are median, box limits are upper and lower quartiles, and whiskers denote the largest and smallest values no more than 1.5 times the interquartile range from the limits. Wilcoxon test 2-sided p-values are presented. * p < 0.01; ** p < 0.0001.

Article Snippet: OCT embedded tissues were cut to 15um sections, blocked with 3% donkey serum, 1% BSA, 0.3% TritonX and then stained with following antibodies (1:100 dilution): SiglecF (catalog number AF1706, R&D Systems), Mertk (catalog number AF591, R&D Systems), Pdgfrb (catalog number 14–1402-82, clone APB5, eBioscience), CD68 (catalog number ab955, clone KP1, Abcam), MafB (catalog number HPA005653, Sigma), PDGF-AA antibody (catalog number 07–1436, Millipore), and Pdgfra antibody (catalog number AF1062, R&D Systems).

Techniques: Expressing, RNA Sequencing, Control, Immunofluorescence, Quantitation Assay, Blocking Assay, Cell Culture

Journal: BMC Immunology

Article Title: Eosinophils may play regionally disparate roles in influencing IgA + plasma cell numbers during large and small intestinal inflammation

doi: 10.1186/s12865-016-0153-0

Figure Lengend Snippet: Siglec F expression post-infection. a ; Quantification of Siglec F + cells from BALB/c naïve mice ( n = 7) and at 21 ( n = 4) and 35 ( n = 5) days and post-infection with T. muris . Representative photos of immunohistochemistry in large intestine tissue from BALB/c ( b ); naïve and ( c ); at 21 days post-infection with T. muris ( n = 4). d ; Quantification of Siglec F + cells from BALB/c naïve mice ( n = 6) and at 10 ( n = 5) and 13 ( n = 4) days post-infection with T. gondii PRU . Representative photos of immunohistochemistry in small intestine tissue from BALB/c ( e ); naïve and ( f ); at 10 days post-infection with T. gondii PRU.* p < 0.05, ** p < 0.01, *** p < 0.001 student’s t -test. Scale Bar represents 50 μm

Article Snippet: For MAdCAM-1 and Siglec F staining the same protocol was used but non-specific binding sites were blocked with 7 % goat serum (Invitrogen), a MAdCAM-1 (5 μg/ml, eBiosciences) or Siglec F primary antibody (5 μg/ml, BD Biosciences) was used followed by a biotinylated secondary goat anti rat Fab’ fragment antibody (1 μg/ml, Santa Cruz).

Techniques: Expressing, Infection, Immunohistochemistry