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TECHNIQUES TO STUDY GENOMES - Coggle Diagram
TECHNIQUES TO STUDY GENOMES
BIOLOGICAL SAMPLE (ADN)
NUCLEIC ACID EXTRACTION
Lisis of the cells --> removed content not interesting
LIBRARY PREPARATION
DNA compatible with the sequencing system
STEPS
DNA fragmentation
Enzymatic reactions
Size selection and clean-up
Amplification
Quantification
SEQUENCING
TYPES
NUCLEIC ACID SEQUENCING
DNA
WGS
Complete DNA sequence (30x)
WES
Exons (1,7% genome) (50-150x)
TARGETED
Groups of genes (panels) (500x)
SHORT READ SEQUENCING
NGS
Illumina technology
by synthesis with fluorescent markers
Ion Torrent
detection of H ions
LONG READ SEQUENCING
bigger size
PacBio
ONT-nanopore
disruption in electrical current
RNA
RNA-Seq
genes acively transcribed and quantification of alternative transcripts
SINGLE CELL TRANSCRIPTOMIC
individual cells
RAMPAGE
identification of TSS and quantification of promoter activity
DNA BINDING AND CHROMATIN MODIFICATION
ChIP- Seq
sequences or genes related to histones
CHROMATIN ACCESSIBILITY
DNAse-Seq
specific for open chromatin and TF binding sites
ATAC-Seq
transportase Tn5
DNA METHYLATION
WGBS
roadmaps of methylation (75% CpG)
RRBS
CCGG sites (12% CpG of genome and 85% CpG promoters)
DNAme array
specific CpG sites (need to know them before)
RNA BINDING
eCLIP
RNA substrates each RBP interacts
RNA Bind-n-seq
quantification of RBP-RNA interactions
3D CHROMATIN STRUCTURE
Hi-C
ChIA-PET
chromatin interactions
QUALITY CONTROL
ALIGNMENT AND ASSSEMBLY
ANALYSIS