whole-genome microarray-based transcriptome profiling using  (Illumina Inc)

Journal: Cell Reports

Article Title: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease

doi: 10.1016/j.celrep.2022.111439

Figure Lengend Snippet: A gradient of cytokine-responsive transcriptional signatures stratifies patients with IBD into distinct molecular phenotypes (A) Activation of cytokine-responsive transcriptional signatures in whole colonic biopsies of patients with UC (UNIFI trial, n = 550) and colonic CD (UNITI2 trial, n = 126) (demographics shown in Table S1 ). Enrichment of cytokine-responsive transcriptional signatures was evaluated in the transcriptome of colonic biopsies using gene set variation analysis. A score of +1 suggests that all transcripts are upregulated, while a score of −1 suggests that all transcripts are downregulated (showing median and interquartile range [IQR], Mann Whitney test, ∗∗∗ p < 0.001). (B, C, and D) Gradient of cytokine-responsive transcriptional signature activation in IBD. Each column represents a single patient. The sum of all four scores per subject is also depicted as the total enrichment score (TES). Columns have been clustered by Euclidean distance (method: average, tree ordering: original, figure generated with ClustVis). Cohorts: UNITI2 (n = 126), UNIFI (UC, n = 550), and PROgECT (UC, n = 84). (E and F) Cytokine-responsive transcriptional signature association to clinical indices of human colonic inflammation in UC (UNIFI cohort, n = 550) and cCD (UNITI2 cohort, n = 126). All clinical data were collected prospectively as part of the trials’ protocol ( Feagan et al., 2016 ; Sands et al., 2019 ; Telesco et al., 2018 ).

Article Snippet: Human intestinal biopsies for whole transcriptome profiling (microarray) , Janssen Pharmaceuticals , UNITI2, NCT01369342 UNIFI, NCT02407236 PROgECT, NCT01988961.

Techniques: Activation Assay, MANN-WHITNEY, Generated

Journal: Cell Reports

Article Title: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease

doi: 10.1016/j.celrep.2022.111439

Figure Lengend Snippet:

Article Snippet: Human intestinal biopsies for whole transcriptome profiling (microarray) , Janssen Pharmaceuticals , UNITI2, NCT01369342 UNIFI, NCT02407236 PROgECT, NCT01988961.

Techniques: Microarray, Recombinant, Cell Recovery, Sequencing, Software

Journal: Physiological Reports

Article Title: Renal stromal miRNAs are required for normal nephrogenesis and glomerular mesangial survival

doi: 10.14814/phy2.12537

Figure Lengend Snippet: Increased apoptosis in FoxD1 GC ; Dicer fl/fl stromal derived cells. (A) ToppFun analysis of differentially expressed transcripts obtained from E18.5 control and FoxD1 GC ; Dicer fl/fl kidneys by microarray showed evidence of increased expression of transcripts associated with apoptosis and dysregulation of the p53 signaling pathway. (B) Quantitative PCR validated the upregulation of Bcl2 l11 (Bim) and genes associated with p53 signaling including Trp53inp1, Bax, Jun, Cdkn1a (p21), Mmp2, and Arid3a in E18.5 FoxD1 GC ; Dicer fl/fl kidneys. n = 6, * P < 0.05, ** P < 0.01, *** P < 0.001. (C) Western blot analysis showed increased levels of BimEL and BimL but normal levels of p53 in E18.5 FoxD1 GC ; Dicer fl/fl kidneys. (D, E) Section immunohistochemistry for confirmed increased and ectopic Bim expression (brown) in the renal stroma and nephron progenitors. (F–K) Section in situ hybridization revealed increased and ubiquitous expression of Trp53inp1, Bax, and p21 in E18.5 FoxD1 GC ; Dicer fl/fl kidneys. (L, M) Immunofluorescence revealed increased aCaspase3 + (green) apoptotic cells in the E18.5 FoxD1 GC ; Dicer fl/fl kidneys. (N–Q) Apoptotic cells were largely localized to Meis1,2,3 + (red) glomerular mesangium and interstitial cells. (R, S) No differences in proliferation based on phosphohistone H3 staining were observed. Immunostaining was performed on at least three control and mutant embryos.

Article Snippet: Whole-transcriptome microarray profiling was performed using an Illumina MouseWG-6 v2.0 chip on three litters of E15.5 and E18.5 kidneys.

Techniques: Derivative Assay, Control, Microarray, Expressing, Real-time Polymerase Chain Reaction, Western Blot, Immunohistochemistry, In Situ Hybridization, Immunofluorescence, Staining, Immunostaining, Mutagenesis