Prerequisites 1. Introduction to Genomics 基因组学
- eukaryotes, prokaryotes, viruses
- 真核生物、原核生物、病毒
- water 70%, protein 15%, RNA 6%, DNA 1%
- genome 基因组
- bacterium, human, plant, virus
- 细菌、人类、植物、病毒
- chromosome 染色体
- plasmid 质粒
- mitochondria 线粒体
- chloroplast 叶绿体
- ploidy 倍性
- 2 copies of the same chromosome, one from each parent
- haploid 单倍体
- diploid 二倍体
- polyploid, triploid, tetraploid
- molecular biology 分子生物学
- DNA, RNA, protein
- nucleotide 核苷酸, amino acid 氨基酸
- gene, genome, transcriptome 转录组, proteome 蛋白质组
- DNA: A-T, C-G
- double helix 双螺旋
- sugar-phosphate backbone 糖磷酸骨架
- 5' to 3' direction
- chromosome, gene, exon 外显子, intron 内含子, promoter 启动子, enhancer 增强子, terminator 终止子
- protein
- encoded by gene
- polymer of amino acid monomers 氨基酸单体聚合物
- cellular functions 细胞功能
- catalysis 催化
- structure 结构
- signalling 信号
- amino acid
- 20 types
- 3-letter and 1-letter code
- hydrophobic 疏水, hydrophilic 亲水, charged 带电
- central dogma
- DNA -> RNA -> protein
- transcription 转录, translation 翻译
- U (uracil) in RNA instead of T (thymine) in DNA
- ribosome 核糖体, tRNA, mRNA
- reserve transcription 逆转录
- mRNA -> DNA
- reverse transcriptase 逆转录酶
- retrovirus 逆转录病毒
- gene
- unit of heredity 遗传单位
- 2% of human genome codes for genes
- promoter, 5' UTR, coding sequence, 3' UTR, terminator
- coding sequence: exon, intron
- variation
- sequence variation
- single nucleotide variation (SNV) 单核苷酸变异
- single nucleotide polymorphism (SNP) 单核苷酸多态性
- indels: insertion, deletion
- structural variation
- large-scale (>50bp)
- involving entire sections of DNA
- gain or loss of fucntion (GoF, LoF)
- conservation
- sequence variation
- sequencing technology
- DNA/RNA extraction -> library preparation -> sequencing -> export fastq files -> QC/analysis
- Illumina, Nanopore
- FASTQ files, reads
- 4 lines per read
- identifier - unique name
- sequence - AGTC
- spacer - +
- quality - confidence score for each DNA base
- 4 lines per read
- sequencing strategies
- whole genome sequencing (WGS)
- all DNA in cells
- whole exome sequencing (WES)
- all exons
- cheap, capture importants
- RNA sequencing (RNA-seq)
- all RNA in cells
- scRNA-seq
- all RNA but idividual cells
- Amplicon
- use PCR target specific region
- Pair-end
- sequence both ends of DNA fragment
- whole genome sequencing (WGS)