Desterke et al, 2020, Heterogeneity of macrophage immunoproteasome activation during lung COVID19 disease

This study describe the activation of immunoproteasome components in M1 polarized macrophages at lung level during COVID19 disease. - Supplemental table 1:Table of genes implicated in MHC class I antigen presentation and found up regulated in COVID19 lung depending of SARS-COV2 virus level detected in the tissue - Supplemental Table 2: Genes found to be significant on PSMB8 cell trajectory inside CD14+/CD68+ bronchoalveolar cells from COVID19 patients - Supplemental Table 3 : Table of allele prevalence for 70 most frequent HLA-A,B,C through 20 ethnicities with worldwide distribution (USA NMDP bone marrow registry) - Supplemental Table 5: SARS-COV2 immunopeptidome against MHC class I presentation through 70 most prevalent HLA-A,B,C allele

NR0B2 regulation during Primary Sclerosing Cholangitis defines a metabolic and pre-malignant reprogramming of Cholangiocyte

Supplemental tables associated to manuscript:Supplemental Table 1. Text mining of the 525 ranked genes found in PUBMED with symptom keywords: this Table describes the 525 ranked genes obtained by text mining with the ‘Génie’ algorithm against the three MESH terms: biliary inflammation, biliary fibrosis and biliary stasis. The respective ranks, p-values and PMID identifiers collected for each gene and each MESH term are presented.Supplemental Table 2. Symptom-related genes found to be differentially expressed in livers from primary sclerosing cholangitis patients: Differentially expressed gene analysis results (logarithmic Fold Change, Average Expression and Adjusted p-values) are presented with respective machine learning predictive scores for supervised sample categories from the GSE61256 dataset (PSC versus other liver samples).Supplemental Table 3. Pavlidis Template Matching for FXR dependency in the liver transcriptome. Results of Pavlidis template analysis used to describe the FXR regulation dependency of PSC genes in liver samples from the GSE54557 dataset. For each gene, the R-Pearson correlation coefficient and its respective p-value are presented in this Table. Supplemental Table 4. Best one hundred genes found to be significant in the pseudotime trajectory of Abcb4-/- cholangiocytes. Best one hundred ranked genes found to be significant on the pseudotime cell trajectory of Abcb4-/- cholangiocytes based on the alternative expression of Nr0b2 and Sox9 in GSE168758.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

PPAR-gamma cistrome repression during activation of lung monocyte-macrophages in severe COVID-19. Desterke et al.

Supplemental tables 3, 4, 5 Supplemental S1 Data (R bioinformatics code) for iscience article ISCIENCE-D-20-0141