diff --git a/README.md b/README.md index 37fec1a8762cc1c037e0791c1ce7c406a218aece..564ef0c6cea11ca0bd1d0808c60d37fa58b42717 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,11 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA sequencing ======================================================================================== -Contact: Gervaise H. Henry -Department: Urology +* Contact: Gervaise H. Henry +* Email: gervaise.henry@gutsouthwestern.edu +* Institution: UT Southwestern Medical Center +* Department: Urology -#Data Analysis +# Data Analysis * Requirements: * 10x CellRanger analyzed data: * "filtered\_gene\_bc\_matrice_mex" folder @@ -31,7 +33,7 @@ Department: Urology * sc_Table (produce tables of population differences between samples) * Genesets - * "regev\_lab\_cell\_cycle\_genes.txt" G2M and S phase genes from **Triosh et al, 2015** + * "regev\_lab\_cell\_cycle\_genes.txt" G2M and S phase genes from [*Genome Res. 2015 Dec; 25(12): 1860–1872*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665007/) * "DEG\_C2.CGP.M10970.txt" MSigDB C2 Chemical and Genetic Perturbations M10970 **CHUANG\_OXIDATIVE\_STRESS\_RESPONSE\_UP** * "DEG\_Epi_2FC.txt" DWS generated DEGs of Epithelia from FACS population (bulk) RNA-sequencing * "DEG\_FMSt_2FC.txt" DWS generated DEGs of Fibromuscular Stroma from FACS population (bulk) RNA-sequencing @@ -41,7 +43,7 @@ Department: Urology * "DEG\_C5.BP.M11704.txt" MSigDB C5 GO Biological Processes M11704 **GO\_CELL\_DIFFERENTIATION** * "DEG\_C5.BP.M10794.txt" MSigDB C5 GO Biological Processes M10794 **GO\_SMOOTH\_MUSCLE\_CELL\_DIFFERENTIATION** * "DEG\_C5.BP.M13024.txt" MSigDB C5 GO Biological Processes M13024 **GO\_REGULATION\_OF\_FIBROBLAST\_PROLIFERATION** - * "EurUrol.2005.NE.txt" Neuroendocrine markers from Table 1 of *"Neuroendocrine differentiation in prostate cancer: implecations for new treatment modalities" European Urology 47.2 (2005): 147:155* + * "EurUrol.2005.NE.txt" Neuroendocrine markers from Table 1 of [*Eur Urol. 2005 Feb;47(2):147-55*](https://www.ncbi.nlm.nih.gov/pubmed/15661408) * "Basal cells-signature-genes.csv" scRNA-Sequencing Lung Map generated top 20 DEGs for human lung Basal Cells * "Normal AT2 cells-signature-genes.csv" scRNA-Sequecing Lung Map generated top 20 DEGs for human lung Alveolar Type 2 Cells * "Club\_Goblet cells-signature-genes.csv" scRNA-Sequencing Lung Map generated top 20 DEGs for human lung Club/Goblet Cells