Single cell analysis on Melanoma (PMID:27124452)

Paper: Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016
Organism: Homo sapiens
Cell type: CD45+/- cells (Melanoma, T-cells, B-cells, Macrophages, NK cell, CAFs and Endothelial cells)
Sample number: 4,645
Library preparation: Smarter
DATA: GSE72056
Analysis:

  1. 25PE/Bowtie(1.4.1) -n 0 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 –S/RSEM
  2. Focus on across all cells combined (average log2(TPM)>4.5) or within
    a single tumor (average log2(TPM)>6 in at least one tumor)

  3. exclude from analysis any cells that did not express at least 2,000 of these 5,948 genes
  4. Inference of CNVs from RNA-seq
  5. tSNE followed by density clustering.
  6. Controlling for inter-tumor differences (???)
  7. PCA (PC1 is technical, PC2 is cell cycle, )
  8. CCND3 in high cell cycle, KDM5B non cycle
  9. PC3&6 is location, PC4&5 is MITF
  10. Variability of T-cell exhaustion related genes (reflect treatment response etc)

Proliferation vs Differentiation in CD4 Th2 condition in vivo&vitro (PMID: 27176874)

Paper: Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. Genome Biology. (2016)
Organism: Mus Musculus
Cell type: CD4 T-cell in vivo and vitro
Sample number: 287
Library preparation: Smarter/C1, 75PE
DATA: E-MTAB-4619
Analysis:

  1. mapped to Ensembl38.70 combined with ERCC / GSNAP / HTSeq / TPM / Poor quality cells are detected by mapping on 37 genes on the mitochondrial genome
  2. Continue reading

My publication on Treg

Immunology

Morikawa, H. et al. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America 111, 5289-5294, doi:10.1073/pnas.1312717110 (2014).
: My recent paper on Regulatory T-cells. This paper show the independent roles of Foxp3 and epigenetic modification of the genome (DNA Methylation). Foxp3 is thought to be the master gene of Regulatory T-cells, but from this paper, Foxp3 is essential for gene regulation of regulatory T-cell, but not sufficient.

Morikawa, H. & Sakaguchi, S. Genetic and epigenetic basis of Treg cell development and function: from a FoxP3-centered view to an epigenome-defined view of natural Treg cells. Immunological reviews 259, 192-205, doi:10.1111/imr.12174 (2014).
: Review article on regulatory T-cell specific gene regulation. Main aim of this review is show the latest general understanding of regulatory T-cell specific gene regulation. Understanding of this is important especially for clinical application of human regulatory T-cell, because human regulatory T-cell easily express Foxp3, but they are not all regulatory T-cells.