Project description:To estimate the reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay we performed the genome-wide correlation analysis of H3K4me2 enrichment patterns from 7 independent standard ChIP-Seq assays (2 million D10 cells), and micro-scaled ChIP-Seq 100,000 cells sample –(N=12), 10,000 cells sample–(N=3), and 1000 cell sample – (N=4)
Project description:Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
Project description:UPLC-HRMS/MS targeted data from the 96 multicomponent reactions related to manzamine synthetic metabolomes. Probes MS/MS spectra and MZmine3 batch files are also provided. Settings: Agilent LC-qTof 6546, ACQUITY UPLC BEH C18 column, 5% to 100% ACN in H2O with 0.1% formic acid, 40eV.
Project description:Cell cycle inhibitors are commonly used drugs against cancer. However, mechanism of developing resistance to this class of drugs is unknown. Retinoblastoma (RB) is a good model to study this process because it is driven by mutations in the core components of cell cycle, i.e, Rb gene. However, there is limited gene expression dataset in RB and reproducibility in standard differential expression analysis is hampered by patient and environment specific variation. To get a diverse human dataset, we performed xenografts and cultured in two different conditions using NCC cell lines. Two different culture conditions were used to grow NCC cell lines: standard tissue culture plates and graphene sponge.
Project description:Isobaric tag-based sample multiplexing strategies are extensively used for global protein abundance profiling. However, such analyses are often confounded by ratio compression resulting from the co-isolation, co-fragmentation, and co-quantification of co-eluting peptides, termed “interference.” Recent analytical strategies incorporating ion mobility and real-time database searching have helped to alleviate interference, yet further assessment is needed. Here, we present the Strain-Specific Peptide (SSP) standard, a TMTpro-tagged reference sample that leverages the genetic variation in the proteomes of eight phylogenetically divergent mouse strains. Typically, a peptide with a missense mutation will have a different mass and retention time than the reference or native peptide. TMT reporter ion signal for the native peptide in strains that encode the mutant peptide suggests interference which can be quantified and assessed using the interference-free index (IFI). We showcase the SSP standard by investigating interference in three common data acquisition methods and by testing the improvements in the IFI when using ion mobility-based gas phase fractionation. In addition, we provide a user-friendly, online viewer to visualize the data and streamline calculation of the IFI. The SSP standard will aid in developing and optimizing isobaric tag-based experiments.
Project description:Unlike genomic alterations, gene expression profiles have not been widely used to refine cancer therapies. We analyzed transcriptional changes in acute myeloid leukemia (AML) cell lines in response to standard first-line AML drugs cytarabine and daunorubicin by means of RNA sequencing. Those changes were highly cell- and treatment-specific. By comparing the changes unique to treatment-sensitive and treatment-resistant AML cells, we enriched for treatment-relevant genes. Those genes were associated with drug response-specific pathways, including calcium ion-dependent exocytosis and chromatin remodeling. Pharmacological mimicking of those changes using EGFR and MEK inhibitors enhanced the response to daunorubicin with minimum standalone cytotoxicity. The synergistic response was observed even in the cell lines beyond those used for the discovery, including a primary AML sample. Additionally, publicly available cytotoxicity data confirmed the synergistic effect of EGFR inhibitors in combination with daunorubicin in all 60 investigated cancer cell lines. In conclusion, we demonstrate the utility of treatment-evoked gene expression changes to formulate rational drug combinations. This approach could improve the standard AML therapy, especially in older patients.
Project description:To estimate the reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay we performed the genome-wide correlation analysis of H3K4me2 enrichment patterns from 7 independent standard ChIP-Seq assays (2 million D10 cells), and micro-scaled ChIP-Seq 100,000 cells sample M-bM-^@M-^S(N=12), 10,000 cells sampleM-bM-^@M-^S(N=3), and 1000 cell sample M-bM-^@M-^S (N=4) Examination of H3K4me2 histone modifications in mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC).