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Collection : Elife (E-Journal - Via Crossref) فلترة بواسطة : عنوان

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Supplementary file 4. Differentially expressed genes (DEGs) with promoterscontaining differentially accessible peaks and discovered IPA categories in nervous system development and function; along with DEGs in the SMARCB1KD group within 500 kB of an LA peak. ; Sheet 1: Differentially expressed genes (q < 0.05, FC > 1.5) with promoters containing differenitally accessible peaks (q < 0.01, FC > 2). Sheet 2: List of IPA categories in Nervous System Development and Function with associated p-values of enrichment and activation scores when considering genes within 500 kb of lower accessibility peaks in SMARCB1KD cells following the neural induction protocol. The category Development of Neurons is highlighted in yellow. Sheet 3: The genes within this category that show significantly different expression in the SMARCB1 KD group and that fall within 500 kB of an LA peak.

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Figure 2—figure supplement 1. Analysis of upstream regulators. ; (A) Top five upstream regulators identified by ingenuity pathway analysis (IPA) of complete proteome dataset (log23×Tg-AD vs. control) at each time point. MAPT (tau), APP and PSEN1 were identified as top upstream regulators. (B) Regulated proteins downstream of MAPT, APP and PSEN1 largely overlap (109). (C) Enrichment analysis (IPA) of overlapping proteins reveals their strong association with mitochondrial dysfunction, cell death and oxidative stress. Data are shown for 18-month-old animals. Orange line indicates the p-value cut-off, p

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Figure 6. Combinatorial treatment induces expression of genes associated with structural maturation. ; (A) Heatmap shows differentially expressed genes in hiPSC-1 myotubes upon combinatorial treatment compared to DMSO from three independent replicates. (B) Table shows muscle differentiation associated transcription factors and miRNAs that were upregulated in combinatorial treatment group when compared to DMSO group as revealed by IPA. (C–D) Bar graphs show the top physiological systems (C) and canonical pathways (D) associated with genes upregulated in combinatorial treatment group when compared to that of DMSO as revealed by IPA. (E–F) Bar graphs show the top biological processes (E) and cellular components (F) associated with genes upregulated upon combinatorial treatment based on gene ontology (GO) analysis. Data are plotted as –log (p-value) in C-F.

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Figure 4. IFNγ is required for development of T-bethi BDN cells and regulates ASC formation and recovery. ; (a) Ingenuity Pathway Analysis (IPA) to identify predicted upstream direct and indirect regulators of the HD BDN Be1 transcriptome. IPA performed using the 427 DEG (BDN Be1 over BDN Be2; FDR < 0.05) identified in the RNA-seq analysis described in Figure 3b. The predicted activation state (z-score of BDN Be1 over BDN Be2) of each regulator/signaling pathway is shown as bar color (orange, activated; blue, inhibited) with predicted upstream regulators sorted in order of significance (overlap P value). Regulators with an overlap P-value

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Figure 2. Comparative proteome analysis of 3×Tg-AD and control samples at different stages of AD. ; (A, B, C) Activation of biological processes at different stages of the disease assessed by Ingenuity Pathway Analysis (IPA). Heat maps represent activation z-score change over the course of disease progression and indicate pathways that are activated at 6M (A), 12M (B) and 18M (C). Data were obtained from four biological replicates per group for each time point. Z-score is calculated based on experimental protein expression data (log2 AD/control ratio) and the theoretical information stored in the IPA Knowledge Base. Positive value of z-score indicates an activation of biological pathway or function. Distribution of the quantified proteins at 2M (D), 6M (E), 12M (F) and 18M (G) based on log2 ratio AD/Control and p-value (t-test) by time point. The pie charts represent the number of quantified non-regulated proteins (grey), significantly different proteins between 3×Tg-AD and control samples, t-test p-value 0.05 (pink) and significantly regulated proteins with more than 50% expression change in comparison to the control (red). (H–I) Dynamics of protein expression over the course of AD progression for a selection of the most regulated proteins based on their function. Proteins involved in mRNA processing and transport (H) that are upregulated over time and serine protease inhibitors (I) that are downregulated. (J–M) Putative presymptomatic protein markers of the disease. (J) Top 10 significantly up- and downregulated proteins in 3×Tg-AD mice at presymptomatic time point (2M). (K) Immunoblot analysis of most regulated hits. Soluble fractions of brain proteins were analyzed from four 2-month-old control and 3×Tg-AD mice animals, respectively. Hebp1 and Glo1 levels were consistently elevated in the transgenic animals as compared to wild type controls. Ca1 levels were reduced in transgenic animals. Presymptomatic markers that remain up- (L) or downregulated (M) across the AD progression.

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Figure 3. SMARCB1 KD prevents neural induction and upregulation of neural differentiation-related genes. ; (A) Top: Control and SMARCB1 KD cells subjected to a 5 day definitive endoderm protocol induction protocol stained for SOX17 (red) and with DAPI (blue). Bottom: Flow cytometry histograms showing similar percentages of CXCR4+ cells in control and SMARCB1 KD cells subjected to this protocol. (B) Top: Control and SMARCB1 KD cells subjected to a 4-day mesodermal induction protocol stained for EOMES (green) and with DAPI (blue). Bottom: qPCR analysis of control and SMARCB1 KD cells subjected to the same protocol for the early mesodermal markers GOOSECOID, HAND1, and FOXF1. All qPCR results are relative to steady state hESCs and are normalized to the geometric mean of 18S and GAPDH levels. (C) Top: Control and SMARCB1 KD cells subjected to a 6 day directed neural induction protocol stained for PAX6 (red), OCT4 (green), and with DAPI (blue). Bottom: qPCR analysis showing a failure of SMARCB1 KD cells to upregulate neural differentiation markers PAX6, CHD2, NESTIN, and MS1. (D) Top: Control and SMARCB1 KD embryoid bodies (EBs) subjected to a neural induction protocol. Bottom: qPCR analysis showing a failure of SMARCB1 KD cells to upregulate the neural differentiation markers PAX6, CHD2, NESTIN, and MS1. (E) Top: Volcano plot illustrating the extent and significance of differential gene expression between control and SMARCB1 KD cells subjected to neural induction protocol as determined by RNAseq (q < 0.01 and FC > 2.0). Bottom: RNAseq tracks PAX6 for steady state hESCs as well as control and SMARCB1 KD cells subjected to a monolayer neural induction protocol. Flat lines indicate undetectable or nearly undetectable expression at the scale used. (F) Top: Activation scores for IPA Nervous System Development sub-categories, considering genes expressed at lower levels in SMARCB1 KD cells compared to controls following the neural induction protocol. Bottom: Activation scores for IPA Embryonic Development sub-categories, considering genes expressed at higher levels in levels in SMARCB1 KD cells compared to controls following the neural induction protocol.

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Figure 8. Changes in the mRNA expression of immune regulated genes in the retina following microglial TGFBR2 ablation using Nanostring-based profiling. ; Four groups of animals (n = 3 animals per group) were analyzed: (1) Control animals not administered tamoxifen, (2) Control animals administered tamoxifen, (3) TG animals 2 weeks after tamoxifen administration, (4) TG animals 8 weeks after tamoxifen administration. (A) Hierarchical clustering of differentially expressed genes showed separate clustering of control and TG animals administered tamoxifen. (B) Volcano plots showing genes that were differentially expressed between control and TG animals administered tamoxifen at 2 and 8 weeks respectively. (C) Gene ontogeny (GO) analysis using IPA demonstrated a number of canonical pathways that were differentially represented between control and TG animals administered tamoxifen at 2 weeks reflecting the activation of neuroinflammatory pathways and pathways involved in immune cell activation and maturation.

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Supplementary file 1. The enriched pathways in Adult Naive, Resolved, and Sensitized mice infected with UPEC for 3.5, 6, or 24 hpi, compared to mock infection. ; Gene fold change cut off for use in IPA analysis is 2-fold or greater; cut off for P value of enrichment is 0.05 or -log10(P value) of 1.3; ‘ratio’ is the number of genes differentially expressed in the samples divided by the number of genes in this pathway; and Z-score is a statistical measure of the match between expected relationship direction and observed gene expression: positive z-score predicts activation, negative z-score predicts suppression.

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Figure 1—figure supplement 1. Physical and transcriptional characteristics of SMARCB1 KD hESCs. ; (A) Protein levels of SMARCC2, SMARCD1, and SMARCE1 following 2 and 3 days of SMARCB1 KD, with Lamin A/C levels as the loading control). (B) The mRNA levels of SOX2, OCT4, and NANOG are shown for cells carrying shRNAs against a negative control region and SMARCB1, both prior to and following 3 days of treatment with 1 µg/µl doxycycline. (C) Bright-field images of cells carrying shRNAs against SMARCB1 both prior to and following 3 days of treatment with 1 µg/µl doxycycline. (D) Top IPA Physiological System Development and Function categories cells subjected to 3 days of SMARCB1 KD. (E) Percentage of genes downregulated following SMARCB1 KD with the indicated histone marks, based on gene sets defined in Pan et al. (2007).

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Figure 5. IL6/IL6R/CEBPB gene module is enriched in active TB transcriptome and proteome and correlates with monocyte expansion. ; (a) Top panel: upstream regulators significantly enriched by causal Ingenuity Pathway Analysis (IPA) in monocyte transcriptomes from patients with active TB (GSE19443), ranked by activation z-score, p-values are corrected for genome-wide testing (FDR). Bottom panel: IRF1 and STAT1 are the top upstream regulators shared between the ‘Berry TB’ disease signature (Berry et al., 2010) (GSE19435, GSE19439, GSE19444), the ‘IL6/STAT3’ pathway (Hallmark GSEA) and the human ‘in vivo IFN-β” signature (GSEA HECKER_IFNB1_TARGETS). (b) Top panel: overlap between the ‘Berry TB’ disease signature, the ‘IL6/STAT3’ pathway and the ‘Scriba plasma TB’ proteomic signature (Scriba et al., 2017) identified ‘IFN/IL6-shared’ and ‘IL6/STAT3-specific’ signatures. Bottom panel: significant STRING protein-protein interaction network (p

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