Quality control figures for ATAC-seq on a mesoderm differentiation dataset

Quality control figures for the ATAC-seq data described in Loh and Chen et al., Cell (http://www.cell.com/cell/abstract/S0092-8674(16)30740-1)

High-throughput surface marker screening data on a mesoderm differentiation dataset

This file contains data from a high-throughput, antibody-based screening of surface markers expressed on various mesodermal progenitors, as described in Loh and Chen et al., Cell (http://www.cell.com/cell/abstract/S0092-8674(16)30740-1). <div><br></div><div>The numbers in this CSV represent the percentage of viable cells (namely, DAPI-negative cells) in each lineage that expressed each given surface marker. These were determined by rigorously gating the PE fluorescent signal such that no more than several percent of negative control cells (unstained cells or cells that were stained with an isotype control antibody directed against no known cellular antigen) were regarded positive.</div

Annotated bulk-population RNA-seq data on a mesoderm differentiation dataset

<div>Bulk-population RNA-seq data as described in Loh and Chen et al., Cell (http://www.cell.com/cell/abstract/S0092-8674(16)30740-1). Each row in this spreadsheet, corresponding to one gene, has been annotated with whether it is associated with the GO code GO:0009986 ("cell surface"). For each pair of cell types that we compare, each row also has two columns ("DE [celltype1]-[celltype2]" and "sLFC [celltype1]-[celltype2]"), which respectively denote whether that gene is differentially expressed in the two cell types and the shrunken log fold change between the two cell types, as calculated by DESeq2 (Love, Huber, Anders (2014)). If the sLFC is negative, it means that the expression of that gene in [celltype1] is lower than in [celltype2]. For brevity, only genes that are differentially expressed in at least one condition have been included.</div><div><br></div><div><div></div></div

INI876690 Supplemental Material1 - Supplemental material for Irradiation or temozolomide chemotherapy enhances anti-CD47 treatment of glioblastoma

Supplemental material, INI876690 Supplemental Material1 for Irradiation or temozolomide chemotherapy enhances anti-CD47 treatment of glioblastoma by Sharareh Gholamin, Osama A Youssef, Marjan Rafat, Rogelio Esparza, Suzana Kahn, Maryam Shahin, Amato J Giaccia, Edward E Graves, Irving Weissman, Siddhartha Mitra and Samuel H Cheshier in Innate Immunity</p

INI876690 Supplemental Material2 - Supplemental material for Irradiation or temozolomide chemotherapy enhances anti-CD47 treatment of glioblastoma

Supplemental material, INI876690 Supplemental Material2 for Irradiation or temozolomide chemotherapy enhances anti-CD47 treatment of glioblastoma by Sharareh Gholamin, Osama A Youssef, Marjan Rafat, Rogelio Esparza, Suzana Kahn, Maryam Shahin, Amato J Giaccia, Edward E Graves, Irving Weissman, Siddhartha Mitra and Samuel H Cheshier in Innate Immunity</p

Influence of anti-CD47 pretreatment of tumor cells or pretreatment of macrophages on phagocytosis; polarization properties of M1 and M2 macrophages after anti-CD47 treatment in vitro.

<p>(A) Bar graph demonstrating Fc-receptor contribution during anti-CD47 treatment. Anti-CD47 mediated phagocytosis is marginally reduced A monoclonal antibody against EGFR (Cetuximab) was used as an inductor of antibody-dependent cellular phagocytosis (ADCP) which is abrogated upon pre-blocking with an Fc-Blocking peptide. (significant difference in means of technical triplicates indicated by * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001, multiple t-tests). (B) Bar graph demonstrating the change in phagocytosis rates by human M0 macrophages towards GBM6 -/+ anti-CD47 pretreatment of tumor cells or pretreatment of macrophages vs. IgG4 isotype-matched control antibody (significant difference in means of technical triplicates indicated by * p ≤ 0.05, multiple t-tests). (C) Overlay contour plots of either resting human M1 or M2 macrophages (CD11b+ CD14+) treated with anti-CD47 antibody or control IgG4 and phagocytosing M1 and M2 macrophages.</p

Cell lines used for <i>in vitro</i> and <i>in vivo</i> experiments, tissue of origin.

<p>Cell lines used for <i>in vitro</i> and <i>in vivo</i> experiments, tissue of origin.</p

Differential phagocytosis rate of mouse M1 and M2 macrophages toward various human glioma cells upon CD47-SIRPα disruption.

<p>(A) Representative flow cytometric phagocytosis assay of mouse M1 macrophages against CSFE-labeled GBM1 and PGBM1 cells. The percentage of CSFE+CD11b+CD80^high live singlets was measured and compared between untreated and anti-CD47 antibody-treated co-cultures. (B) Representative flow cytometric phagocytosis assay of mouse M2 macrophages against CSFE-labeled GBM1 and PGBM1 cells. The percentage of CSFE+CD11b+CD206^high live singlets was measured and compared between untreated (left column) and anti-CD47 antibody-treated (right column) co-cultures. (C) Bar graph demonstrating the change in phagocytosis rates by mouse M1 macrophages towards individual co-incubated cell lines (GBM1, GBM4 and PGBM1) -/+ anti-CD47 (significant difference in means of technical triplicates indicated by * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001, multiple t-tests). (D) Bar graph demonstrating the change in phagocytosis rates by mouse M2 macrophages towards individual co-incubated cell lines (GBM1, GBM4 and PGBM1) -/+ anti-CD47 (significant difference in means of technical triplicates indicated by * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001, multiple t-tests).</p

CD47 expression of the tested cell lines.

<p>CD47 expression of the tested cell lines.</p

M1 and M2 macrophage phagocytosis rates after anti-CD47 treatment.

<p>Data are means of 3 replicates per tumor cell line.</p