Time and space 2

Methods

• Genomics, transcriptomics
  • Fragmentation -> Labeling (adaptors - primers - p7,p5+"barcodes")
  • PCR amplification
  • Ilumina sequencing - attaching - cluster amplification - measurement of fluorescence
• Whole genome
• vs exome
  • Fragments - hybridization - pullout - sequencing of exome fragments
• Transcriptome
  • qPCR - need for specific gene
  • bulk RNA
  • scRNA
  • nanostring - target + capture probe + amplification probe
  • RNA seq - reverse transcriptase > ilumina
    • mRNA vs premRNA
    • mRNA - selected by poly A
    • pre - rRNA depletion
  • scRNA
    • expensive
    • thoudsands - mil cells
    • polya seleection
    • filtering - dead cells - higher mito RNA levels
    • spatial transcriptomics
• Genomic assays -
  • CHIP
  • Reporter assay
    • jaspar - tf binding database-
• Cut and tag, cut and run
• clinical - severity prediction - polypheh