Exemplary validation of newly identified p53 target genes.

Slides:

Advertisements

Similar presentations

Correlation of log-transformed signal intensity from two Affymetrix microarray hybridizations using platelet RNA. Plotted are those probesets with an average.

Advertisements

Sequence alignment of C-terminal phosphorylated plant aquaporins

Experimental overview A sequential protein and peptide IMAC enrichment was analyzed by four different LC-MS/MS strategies. Experimental overview A sequential.

Distribution of phosphorylation sites identified in the cytosolic phosphoproteome.A, numbers of approved phosphopeptides, previously phosphorylated peptides,

Microvesicles released by PC-3 cells.

Classification of proteins in PC-3 cell-released microvesicles by GOslim annotations. Classification of proteins in PC-3 cell-released microvesicles by.

Percentage of proteins identified in envelope membrane extracts according to the purification method and the number of transmembrane domains. Percentage.

Differential conjugation of endogenous SUMO-1 and endogenous SUMO-2/3 to target proteins.A and B, SUMO-1 and SUMO-2 proteins were produced in E coli and.

Frequency distribution of the GRAVY of the theoretical proteins (open bars) and of 110 genes encoding proteins identified on a 2-D electrophoresis gel,

Relative quantitation of phosphopeptides from conditioned media from subtype specific breast cancer cell lines. Relative quantitation of phosphopeptides.

Complementary identification and novel protein discovery

Visual validation of the computational outputs.

Schematic representation of proteogenomic annotation strategy.

Novel p53 target genes identified by RNA-Seq, pSILAC and ChIP-Seq.

Assay of NOS activity. Assay of NOS activity. Box show total NOS activity, the calcium-dependent activity of the constitutive isoforms of NOS (eNOS and.

Expression of apocrine markers at various stages of apocrine carcinoma progression. Expression of apocrine markers at various stages of apocrine carcinoma.

Workflow of the integrated proteomics approach to identify the abnormal network in NF1-KD PC12 cells. Workflow of the integrated proteomics approach to.

Bottom-up proteomic characterization of MALDI IMS samples.

Genome-wide analysis of p53 occupancy.

Success rates in validation of antibodies from external providers

Results from the Morris water task.

Degree of glycosylation of human milk LF from individual donors across lactation. Degree of glycosylation of human milk LF from individual donors across.

Cluster analysis and pathway-based characterization of differentially expressed genes and proteins from integrated proteomics. Cluster analysis and pathway-based.

BIRC6 is expressed in the tumorigenic Aldefluorhigh fraction of colonosphere cells. BIRC6 is expressed in the tumorigenic Aldefluorhigh fraction of colonosphere.

Colonopshere-enriched proteins display functional interactions.

Identification of SUMO3peptides from 2D-LC-MS/MS analyses of a tryptic digest of HEK293-SUMO3 cells using DDA and DIA methods. Identification of SUMO3peptides.

Proteins previously reported in published MALDI IMS studies and their frequency of observation in the present study. Proteins previously reported in published.

Schematic model of effector pathways that mediate tumor suppression by p53. Schematic model of effector pathways that mediate tumor suppression by p53.

MRNAs that show increased protein synthesis following UPF1 depletion are enriched for those with very long 3′UTRs. mRNAs that show increased protein synthesis.

High correlation of expression changes of NMD-regulated genes identified by both the pSILAC screen and previously reported global RNA screens after UPF1.

Metabolic pathway alterations in PCT

Analysis of newly synthesized proteins by combined pulsed SILAC and click chemistry enrichment. Analysis of newly synthesized proteins by combined pulsed.

Schematic summarizing the various functions and features of MASH Suite Pro. Schematic summarizing the various functions and features of MASH Suite Pro.

Changes in bacterial adhesion with hmLF addition and the purified glycan from hmLF. Changes in bacterial adhesion with hmLF addition and the purified glycan.

Validation of p53- and miRNA-mediated down-regulation

Altered pathways in prostate cancer.

Resolution and mass accuracy of A, a peptide isotope cluster (m/z 558

Putative targets of miRNAs directly induced by p53 with down-regulated mRNA- and de novo protein synthesis or reduced de novo protein synthesis only. Putative.

Interaction networks of the regulated phosphoproteins.

IEF 2D PAGE of whole protein extracts from breast apocrine macrocysts

LC-MS/MS analyses of synthetic peptides with SUMO1 and SUMO3 remnant chains using ETD, CID, and HCD activation modes. LC-MS/MS analyses of synthetic peptides.

The PPAR-α agonist GW7647 reduces experimentally induced myopia.

Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum. Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum.A,

Plot of the deviation of the predicted pI value of every peptide spectrum from the average pI calculated for each fraction for validated (a) and non-validated.

Distribution of the phosphoproteins based on GO analysis, including biological process (Left) and cellular component (Right). Distribution of the phosphoproteins.

A, Absolute ion intensities of m/z 322, 922 and 1522 as function of the transfer time. A, Absolute ion intensities of m/z 322, 922 and 1522 as function.

Differential expression of apoA-I and Vimentin on 2D gels

K-Means clustering of protein and mRNA expression patterns after PPAR agonists treatments. k-Means clustering of protein and mRNA expression patterns after.

Number of genes/antibodies included in the database.

Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a as compared with the strain MW001. Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a.

Bar plot representation of the transcriptomic changes in Δsaci_ptp and Δsaci_pp2a. Bar plot representation of the transcriptomic changes in Δsaci_ptp and.

Localization of selected clones in mammalian COS-7 cells.

Differential expression levels of archaella operon genes and respiratory chain genes in Δsaci_pp2a and Δsaci_ptp. Differential expression levels of archaella.

Biochemical characterization of the protein phosphatases Saci-PTP.

Voronoi treemaps (109) comparing protein expression profiles of M

Changes in mRNA levels do not correlate with changes in protein levels in upf1Δ and xrn1Δ cells. Changes in mRNA levels do not correlate with changes in.

Illustration of chromatography metric C-2A applied to LC-MS/MS data from three Thermo LTQ systems in analyses of yeast proteome samples in CPTAC Study.

Image analysis and HER-2/neu slide scoring.

Classification of the 1458 identified proteins into molecular functions. Classification of the 1458 identified proteins into molecular functions. The pie.

Separation of colonospheres from differentiated tumor cells by cluster analysis. Separation of colonospheres from differentiated tumor cells by cluster.

Illustration of σ down-regulation in bladder carcinomas.

Enlargements of 2-D gels visualized by Coomassie Brilliant Blue staining. Enlargements of 2-D gels visualized by Coomassie Brilliant Blue staining. In.

Expression of σ in SCCs Expression of σ in SCCs. Shown is a magnified section of a representative 2D PAGE gel run with a lysate from an SCC.

Western blotting analysis of purified cytoplasmic membranes.

Eight serum analytes with greatest differences in levels between clinically infected and non-infected neonates. Eight serum analytes with greatest differences.

Overlap between changes in de novo protein synthesis after p53- or miR-34a-induction. Overlap between changes in de novo protein synthesis after p53- or.

Changes in protein expression during distinct stages of NK cell differentiation. Changes in protein expression during distinct stages of NK cell differentiation.

The average median S.D. and PEV reduction after applying different normalization methods compared with raw data. The average median S.D. and PEV reduction.

Occurrence of fur−-only genes and expected sensitivity to Fur.

Differential protein, mRNA, lncRNA and miRNA regulation by p53.

Presentation transcript:

Exemplary validation of newly identified p53 target genes. Exemplary validation of newly identified p53 target genes.A, qPCR analyses of MDFI, ST14, LINC01021 and miR-486 expression in SW480/pRTR-p53-VSV cells after addition of DOX for the indicated periods of time. B, qChIP validation of p53 occupancy at the MDFI, ST14, LINC01021 and miR-486 promoters in SW480/pRTR-p53-VSV after 16 h of DOX treatment and subsequent VSV-ChIP. C, p53-VSV-derived ChIP-Seq results are displayed using the UCSC genome browser. D, SW480/pRTR-LINC01021_A cell pools were subjected to impedance measurement. Twenty-four hours after seeding, DOX was added as indicated by the dotted line. E, Cell counting using trypan blue exclusion. Results in (A), (B), (D), and (E) represent the mean ± S.D. (n = 3). Sabine Hünten et al. Mol Cell Proteomics 2015;14:2609-2629 © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.