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Title:           Multi-scale signaling and tumor evolution in high-grade gliomas
Subject:         Cancer Cell, 42 (2024) 1217-1238.e19. doi:10.1016/j.ccell.2024.06.004
Author:          Jingxian Liu
Creator:         Elsevier
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     Item: 
      Title: Multi-scale signaling and tumor evolution in high-grade gliomas
      Destination: titlink1
      Children: 
       Item: 
        Title: Introduction
        Destination: flink1
       Item: 
        Title: Results
        Destination: flink2
        Children: 
         Item: 
          Title: High-grade glioma evolution from diagnosis to recurrence is associated with genomic and proteomic drivers
          Destination: slink1
         Item: 
          Title: Tumor-intrinsic and TME-associated features in primary and recurrent high-grade glioma
          Destination: slink2
         Item: 
          Title: Impact and association of genetic alterations on proteomics and metabolomics in HGG
          Destination: slink3
         Item: 
          Title: Associations between glycosylation and phosphorylation in EGFR activities and tumor recurrence
          Destination: slink4
         Item: 
          Title: Protein-protein interaction analysis assisted by targeted proteomics and the Kinase Library identifies pathway disruptions
          Destination: slink5
         Item: 
          Title: PTPN11 may serve as a network hub for EGFR, PDGFRA, and IDH1 signaling
          Destination: slink6
         Item: 
          Title: Metabolic enzymes/pathways connected to RTK activation and dysregulated hypoxia signaling in IDH-mutant HGG
          Destination: slink7
       Item: 
        Title: Discussion
        Destination: flink3
       Item: 
        Title: Supplemental information
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       Item: 
        Title: Consortia
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       Item: 
        Title: Acknowledgments
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       Item: 
        Title: Author contributions
        Destination: acklink2
       Item: 
        Title: Declaration of interests
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       Item: 
        Title: References
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       Item: 
        Title: STAR★Methods
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          Title: Key resources table
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         Item: 
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           Item: 
            Title: Materials availability
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           Item: 
            Title: Data and code availability
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         Item: 
          Title: Experimental model and study participant details
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           Item: 
            Title: Human participants
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         Item: 
          Title: Method details
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           Item: 
            Title: Sample processing
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           Item: 
            Title: Longitudinal cohort sample collection and processing
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           Item: 
            Title: Sample processing for genomic DNA and total RNA extraction
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           Item: 
            Title: Whole exome sequencing
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              Title: Library construction
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             Item: 
              Title: In-solution hybrid selection
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             Item: 
              Title: Preparation of libraries for cluster amplification and sequencing
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             Item: 
              Title: Cluster amplification and sequencing
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           Item: 
            Title: PCR-free whole genome sequencing
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             Item: 
              Title: Preparation of libraries for cluster amplification and sequencing
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             Item: 
              Title: Cluster amplification and sequencing (HiSeq X)
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           Item: 
            Title: Illumina infinium methylationEPIC beadchip array
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           Item: 
            Title: RNA sequencing
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             Item: 
              Title: Quality assurance and quality control of RNA analytes
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             Item: 
              Title: Total RNA-seq library construction
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             Item: 
              Title: Total RNA sequencing
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             Item: 
              Title: miRNA-seq library construction
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             Item: 
              Title: miRNA sequencing
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           Item: 
            Title: Single-nuclei multiome library construction and sequencing
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           Item: 
            Title: MS sample processing and data collection
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             Item: 
              Title: Protein extraction and tandem Lys-C/trypsin digestion
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             Item: 
              Title: TMT-11 labeling
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              Title: Peptide fractionation
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             Item: 
              Title: Phosphopeptide enrichment using IMAC
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             Item: 
              Title: Immunoaffinity purification of acetylated peptides
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             Item: 
              Title: Enrichment of intact glycopeptides
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              Title: LC-MS/MS analysis
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            Title: Polar metabolites and lipid mass spectrometry
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             Item: 
              Title: Metabolite and lipid extraction
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              Title: Chemical derivatization of polar metabolites
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              Title: GC-MS analysis
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              Title: LC-MS analysis
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              Title: Metabolite identification and data processing
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              Title: Lipid identification and data processing
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              Title: Phosphopeptides enrichment by IMAC
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              Title: LC-SRM data acquisition
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            Title: Cell line construction
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            Title: Co-detection by indexing (CODEX) multiplexed tissue imaging
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           Item: 
            Title: Genomic data analysis
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             Item: 
              Title: Harmonized genome alignment
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             Item: 
              Title: Copy number variant calling
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              Title: Somatic variant calling
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             Item: 
              Title: TERT promoter hotspot mutation calling
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             Item: 
              Title: DNA methylation microarray processing
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             Item: 
              Title: Classification of MGMT promoter DNA methylation status
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            Title: RNA quantification and analysis
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             Item: 
              Title: RNA quantification
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              Title: miRNA quantification
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             Item: 
              Title: snRNA/snATAC-seq data preprocessing
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              Title: Peak calling for snATAC-seq data
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             Item: 
              Title: Single-nuclei sequencing cell type annotation
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             Item: 
              Title: snRNA-seq analysis
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             Item: 
              Title: snATAC-seq malignant peak-expression link
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             Item: 
              Title: snATAC-seq differential accessibility analysis
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             Item: 
              Title: snATAC-seq motif enrichment analysis
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             Item: 
              Title: Mapping mutations to snRNA data
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           Item: 
            Title: MS data interpretation
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            Children: 
             Item: 
              Title: Quantification of TMT global proteomics data
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              Title: Quantification of phosphopeptides
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              Title: Quantification of acetylated peptides
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              Title: SRM quantification
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             Item: 
              Title: Normalization of metabolome and lipidome
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              Title: Quantification of intact glycopeptides
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    Title: Multi-scale signaling and tumor evolution in high-grade gliomas
    Author: Jingxian Liu
    Subject: Cancer Cell, 42 (2024) 1217-1238.e19. doi:10.1016/j.ccell.2024.06.004
    Creator: Elsevier
    CreationDate: Mon Feb 10 13:00:07 CET 2025
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   Type: CRC32
  Checksum: e3d530aaf326b34ec2a581152109ed0e
   Type: MD5
  Checksum: 062118cc37ad1981dd2fffd6e9c8d09d3f49916e
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   Type: SHA-256