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......@@ -10,21 +10,16 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA se
* PI: Douglas W. Strand, PhD
* <a href="https://orcid.org/0000-0002-0746-927X" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0002-0746-927X</a>
* PI Email: [douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
* **ANALYZED DATA FOR QUERYING AT: [StrandLab.net](http://strandlab.net/analysis.php)**
* **Raw data at: [GEO (scRNA-Seq)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403) & [GEO (popRNA-Seq)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117271) & [GenitoUrinary Development Molecular Anatomy Project (GUDMAP)]("https://doi.org/10.25548/W-R8CM")**
* **Publication at: PENDING**
Data Analysis
-------------
* **Requirements:**
* /analysis/DATA/D17PrF/
* D17PrF-demultiplex.csv
* 10x/
* aggregation_csv.csv
* GRCh38/
* "barcodes.tsv"
* "genes.tsv"
* "matrix.mtx"
* /analysis/DATA/D27PrF/
* D27PrF-demultiplex.csv
* /analysis/DATA/
* Pd-demultiplex.csv
* 10x/
* aggregation_csv.csv
* GRCh38/
......@@ -46,12 +41,15 @@ Data Analysis
* RColorBrewer (v1.1-2)
* monocle (v2.6.3)
* dplyr (v0.7.6)
* viridis (v0.5.1)
* *and all dependencies*
* **HOW TO RUN**
* 1 Patient D17PrF
* run bash script sc_TissueMapper-D17PrF.sh
* 2 Patients D17PrF and D27PrF
* run bash script sc_TissueMapper-DPrF2.sh
* 1 Run on 3 patient aggregate
* run bash script [sc\_TissueMapper\-Pr.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-Pd.sh)
* 2 Run on 1st patent FACS samples
* run bash script [sc\_TissueMapper\-D17\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D17_FACS.sh)
* 3 Run on 2nd patient FACS samples
* run bash script [sc\_TissueMapper\-D27\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D27_FACS.sh)
* **Pipeline:**
* Link cellranger count/aggr output to analysis
* Create demultiplex file to add custom sample groups
......@@ -61,8 +59,8 @@ Data Analysis
* Load cellranger data into R/Seurat
* Label cells based on their cell cycle stated using Seurat based method
* QC and filter cells/genes
* *If combining multiple experiments:* Align experiments using canonical correlation analysis (CCA)
* Perform principle component analysis (PCA) using most highly variable genes (HVG) for downstream clustering etc
* *If analyzing samples from multiple patients:* Align experiments using canonical correlation analysis (CCA)
* *If analyzing samples from one patient:* Perform principle component analysis (PCA) using most highly variable genes (HVG) for downstream clustering etc
* Perform initial "over" clustering
* Identify "highly stressed" cells using custom PCA based analysis, remove stressed clusters/cells, and re-cluster
* Correlate cluster gene expression using Quantitative Set Analysis for Gene Expression (QuSAGE) on lineage genesets for identification (epithelia, and stroma)
......@@ -82,36 +80,40 @@ Data Analysis
* "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/)
* Stress:
* "DEG\_C2.CGP.M10970.txt" MSigDB C2 Chemical and Genetic Perturbations M10970 [**CHUANG\_OXIDATIVE\_STRESS\_RESPONSE\_UP**](http://software.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_UP.html)
* "genes.deg.Stress.csv" DWS generated DEGs of stressed cells from scRNA-Seq of patient D17 only
* "" DWS generated DEGs of stressed cells from scRNA-Seq of an aggregation of patient D17 and D27
* "genes.deg.Stress.csv" DWS generated DEGs of stressed cells from scRNA-Seq of 3 patient aggregate
* Lineage:
* "DEG\_Epi_5FC.txt" DWS generated DEGs of epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_FMSt_5FC.txt" DWS generated DEGs of fibromuscular stroma from FACS population (bulk) RNA-sequencing
* "genes.deg.Epi.csv" DWS generated DEGs of epithelial cells from scRNA-Seq of patient D17 only
* "genes.deg.St.csv" DWS generated DEGs of stromal cells from scRNA-Seq of patient D17 only
* "" DWS generated DEGs of epithelial cells from from scRNA-Seq of an aggregation of patient D17 and D27
* "" DWS generated DEGs of stromal cells from scRNA-Seq of an aggregation of patient D17 and D27
* "genes.deg.Epi.csv" DWS generated DEGs of epithelial cells from scRNA-Seq of 3 patient aggregate
* "genes.deg.St.csv" DWS generated DEGs of stromal cells from scRNA-Seq of 3 patient aggregate
* Epithelia:
* "DEG\_BE_5FC.txt" DWS generated DEGs of basal epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_LE_5FC.txt" DWS generated DEGs of luminal epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_OE_5FC.txt" DWS generated DEGs of "other" epithelia from FACS population (bulk) RNA-sequencing
* "genes.deg.BE.csv" DWS generated DEGs of basal epithelial cells from scRNA-Seq of patient D17 only
* "genes.deg.LE.csv" DWS generated DEGs of luminal epithelial cells from scRNA-Seq of patient D17 only
* "genes.deg.OE1.csv" DWS generated DEGs of "other" epithelia cluster 1 cells from scRNA-Seq of patient D17 only
* "genes.deg.OE2.csv" DWS generated DEGs of "other" epithelia cluster 2 cells from scRNA-Seq of patient D17 only
* "genes.deg.BE.csv" DWS generated DEGs of basal epithelial cells from scRNA-Seq of 3 patient aggregate
* "genes.deg.LE.csv" DWS generated DEGs of luminal epithelial cells from scRNA-Seq of 3 patient aggregate
* "genes.deg.OE1.csv" DWS generated DEGs of "other" epithelia cluster 1 cells from scRNA-Seq of 3 patient aggregate
* "genes.deg.OE2.csv" DWS generated DEGs of "other" epithelia cluster 2 cells from scRNA-Seq of 3 patient aggregate
* Stroma:
* "DEG\_C5.BP.M11704.txt" MSigDB C5 GO Biological Processes M11704 [**GO\_ENDOTHELIAL\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_ENDOTHELIAL_CELL_DIFFERENTIATION.html)
* "DEG\_C5.BP.M10794.txt" MSigDB C5 GO Biological Processes M10794 [**GO\_SMOOTH\_MUSCLE\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_SMOOTH_MUSCLE_CELL_DIFFERENTIATION.html)
* "DEG\_C5.BP.M13024.txt" MSigDB C5 GO Biological Processes M13024 [**GO\_REGULATION\_OF\_FIBROBLAST\_PROLIFERATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_REGULATION_OF_FIBROBLAST_PROLIFERATION.html)
* "DEG\_C5.BP.M10124.txt" MSigDB C5 GO Biological Processes M10124 [**GO\_LEUKOCYTE\_ACTIVATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_LEUKOCYTE_ACTIVATION.html)
* "genes.deg.Fib.csv" DWS generated DEGs of fibroblast cells from scRNA-Seq of 3 patient aggregate
* "genes.deg.SM.csv" DWS generated DEGs of smooth muscle cells from scRNA-Seq of 3 patient aggregate
* "genes.deg.Endo.csv" DWS generated DEGs of endothelial ccells from scRNA-Seq of 3 patient aggregate
* "genes.deg.Leu.csv" DWS generated DEGs of leukocyte cells from scRNA-Seq of 3 patient aggregate
* Neuroendocrine:
* "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)
* "genes.deg.NE.csv" DWS generated DEGs of neuroendocrine epithelial cells from scRNA-Seq of patient D17 only
* "" DWS generated DEGs of neuroendocrine epithelial cells from scRNA-Seq of patient D17 only
* "genes.deg.NE.csv" DWS generated DEGs of neuroendocrine epithelial cells from scRNA-Seq of 3 patient aggregate
* Lung epithelia from [Lung Gene Expression Analysis (LGEA) Web Portal](https://research.cchmc.org/pbge/lunggens/mainportal.html):
* "Basal cells-signature-genes.csv" scRNA-Seq LGEA generated top 20 DEGs for [human lung Basal Cells] (https://research.cchmc.org/pbge/lunggens/lungDisease/celltype_IPF.html?cid=3)
* "Normal AT2 cells-signature-genes.csv" scRNA-Sequecing LGEA generated top 20 DEGs for [human lung Alveolar Type 2 Cells](https://research.cchmc.org/pbge/lunggens/lungDisease/celltype_IPF.html?cid=1)
* "Club\_Goblet cells-signature-genes.csv" scRNA-Sequencing LGEA generated top 20 DEGs for [human lung Club/Goblet Cells](https://research.cchmc.org/pbge/lunggens/lungDisease/celltype_IPF.html?cid=4)
* Lung epithelia from [*Nature 2018 Aug;560(7718):319*](https://doi.org/10.1038/s41586-018-0393-7)
* "SupTab3\_Consensus\_Sigs.csv" scRNA-Sequencing DEGs of mouse basal, club, ciliated, tuft, neuroendocrine, ionocyte cells (Supplementary Tables, SupTab3\_Consensus\_Sigs)
* "SupTab6\_Krt13\_Hillock.csv" scRNA-Sequencing DEGs of mouse Krt13+ hillock cells (Supplementary Tables, SupTab6\_Krt13\_Hillock)
* "Ensemble.mus-hum.txt" Ensemble export of mouse (GRCm38.p6) to human ortholog mapping
* General MSigDb
* "c2.all.v6.1.symbols.gmt" MSigDB C2 Curated Gene Sets [**MSigDB C2**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=C2)
* "c2.cp.kegg.v6.1.symbols" MSigDB C2 KEGG Gene Subsets [**KEGG**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=CP:KEGG)
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