Data

Web Tools for Exploring Our Single Cell RNA-seq Data

A. Data associated with Park et al. Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage. Cell Rep 2020 32(8):108077

Paper Link: Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage

*** For gene names, please type the official gene symbol approved by the HUGO Gene Nomenclature Committee (e.g. CDKN1A, MDM2).

RShiny tools for exploring scRNA-seq dataset on RKO cells treated with different doses of 5FU.

(1) 2-dimensional analyses (t-SNE, UMAP & individual gene expression) on scaled data & magic-imputed data

http://shiny.sph.umich.edu/hmkang/RSH/RKO2D

(2) Analysis of single cell gene expression across different subgroups of cells partitioned with 5FU dose and group identity, expressed as mean±SEM.

http://shiny.sph.umich.edu/hmkang/RSH/RKOgraph

RShiny tools for exploring scRNA-seq dataset on HCT116 cells treated with different doses of 5FU.

(3) 2-dimensional analyses (t-SNE and UMAP) on scaled data

http://shiny.sph.umich.edu/hmkang/RSH/HCT1162D

(4) Analysis of single cell gene expression across different subgroups of cells partitioned with 5FU dose and group identity, expressed as mean±SEM.

http://shiny.sph.umich.edu/hmkang/RSH/HCT116graph

RShiny tools for exploring scRNA-seq dataset on SW480 cells treated with different doses of 5FU.

(5) 2-dimensional analyses (t-SNE and UMAP) on scaled data

http://shiny.sph.umich.edu/hmkang/RSH/SW4802D

(6) Analysis of single cell gene expression across entire population treated with different 5FU dose, expressed as mean±SEM.

http://shiny.sph.umich.edu/hmkang/RSH/SW480graph/

B. Data associated with Park et al. Holistic characterization of single hepatocyte transcriptome responses to high fat diet. Am J Physiol Endocrinol Metab. 2020 doi: 10.1152/ajpendo.00391.2020.

Paper Link: Holistic characterization of single hepatocyte transcriptome responses to high fat diet

*** For gene names, please type the official gene symbol approved by the Mouse Genome Informatics Database (e.g. Alb, Cyp2f2, Elovl5)

RShiny tools for exploring scRNA-seq dataset on mouse hepatocytes isolated from LFD and HFD livers.

(1) 2-dimensional analyses (PCA, t-SNE, UMAP & individual gene expression) on scaled data & magic-imputed data.

http://shiny.sph.umich.edu/hmkang/leeju_LFD_HFD/magic/

(2) 2-dimensional analyses (PCA, t-SNE, UMAP & individual gene expression) on scaled data & saver-imputed data.

http://shiny.sph.umich.edu/hmkang/leeju_LFD_HFD/saver/

(3) 3-dimensional PCA analysis on scaled data & magic-imputed data.

http://shiny.sph.umich.edu/hmkang/leeju_LFD_HFD/3D/

(4) Analysis of single cell gene expression in hepatocytes of each zone, expressed as mean±SEM.

http://shiny.sph.umich.edu/hmkang/leeju_LFD_HFD/zone/