Resources
Plasmids
Animal Strains
https://bdsc.indiana.edu/index.html
91226 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-FLAG-Atg17}ZH-22A/CyO
91227 Atg17[3F5]/TM6B, Tb[1]
91228 Df(3R)Atg17[4G7]/TM6B, Tb[1]
91229 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-hATG5.WT.FLAG}ZH-51D
91230 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-hATG5.E122D.FLAG}ZH-51D
91231 w[1118]; Df(2R)Sesn-8A11/CyO
91232 w[1118]; Sesn[3F6]/CyO
91233 w[*]; P{w[+mC]=UAS-Sesn.MYC}A3
91234 w[*]; P{w[+mC]=UAS-Sesn.MYC.C86S}2
91235 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-Sesn.FLAG}ZH-86Fa
91236 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-Sesn.CS.FLAG}ZH-86Fa
91237 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-Sesn.DA.FLAG}ZH-86Fa
91238 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-Sesn.DDAA.FLAG}ZH-86Fa
91239 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-gig.K}ZH-22A/CyO
91240 w[*]; M{RFP[3xP3.PB] w[+mC]=UAS-gig.S1338A}ZH-22A
91419 Atg5[5cc5]/FM7i, P{w[+mC]=ActGFP}JMR3
Web Tools for Exploring Our Single Cell RNA-seq Data
Note: In light of recent cyberattack incidents at the University of Michigan, RShiny services appear to be non-functional for public use. We recommend that investigators utilize our GitHub repository to do the relevant analyses as an alternative (https://github.com/leeju-umich/Park_et_al_Cell_Reports_2020), which contains the source codes and data necessary to run these applications.
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.