RNA-Seq data, part II
CSE 180
Yana Safonova
RNA-seq technologies
RNA-seq pipelines
A survey of best practices for RNA-seq data analysis, review, Gen Biol
Finding isoforms using genome mapping
Coverage-based finding isoforms
Isoforms Coverage
ACD 10
ACE 100
BCD 5
BCE 5
Coverage-based finding isoforms
Isoforms Coverage
ACD 10
ACE 100
BCD 5
BCE 5
5 + 5
10 + 100 + 5 + 5
10 + 100
5 + 100
5 + 10
Coverage-based finding isoforms
Isoforms
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5 + 5
10 + 100 + 5 + 5
10 + 100
5 + 100
5 + 10
Splice graph
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
De novo transcriptome assembly
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Differential expression of isoforms / genes
Hepatitis C-associated mixed cryoglobulinemic vasculitis induces differential gene expression in peripheral mononuclear cells
Cell sorting and differential expression of genes
Ellebedy et al, Nat Immunol, 2016 detected a new type of cells using differential expression
Single cell RNA-seq (scRNA-seq)
droplet barcode
molecular barcode
primers
Barcoded RNAs
Droplet barcoding
scRNA-seq visualization
| Sample1 | Sample2 | Sample3 | Sample4 | Sample4 |
Gene1 | ... | ... | ... | ... | ... |
Gene2 | ... | ... | ... | ... | ... |
Gene3 | ... | ... | ... | ... | ... |
PCA
Principal Component Analysis transforms N-dimensional data (that are hard to visualize) to 2-dimensional data preserving “natural clusters” of original points
Bad choice of features
Good choice of features
PCA example: amino acid properties
From 23 features to 11 features
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10
11
10x Cell Ranger
Example cell clustering based differential expression of PBMC from a healthy donor (method t-SNE):
http://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_10k_v3/pbmc_10k_v3_web_summary.html
Gene networks
Proteomics
Proteogenomics
Methods, Tools and Current Perspectives in Proteogenomics
Proteogenomics
CNA - copy number aberrations
eQTL - expression quantitative trait loci
PTM - post translational modification
Methods, Tools and Current Perspectives in Proteogenomics
Correlation between RNA levels and number of proteins
Gene‐specific correlation of RNA and protein levels in human cells and tissues
Proteogenomics example: colorectal cancer
Methods, Tools and Current Perspectives in Proteogenomics