Defining the clusters

[XpelC]

Clean the dataset

• [x] Eliminate the doublet.

cell type name formatting

• [x] Two columns: one column is original cell type names, the other column is the formatted names.

• [x] These name should be lower case, with no space, singular (eliminate inconsistency)

• [x] Left join the table with the data.

Check the dataset:

• [x] To see which sample is from cancer patients, which is not (print a table).
• [x] Check the scRNA sequencing method (10X, SMARTseq2)
• [ ] Check if the count from all dataset are raw count (plot the log + 1 counts densitied ghroup by sample, color by dataset (ggplot))
• [ ] Check which counts are "raw" (integers) and which have decimals, we should avoid to transform the data twice.
• [ ] Color the umap by cancer and normal sample.
• [x] FeaturePlot: Use the original umap (split by cell marker, and sample).
• Use features and the markers:
• "CD14", "FCGR3A", "CD79A", "CD3G" for monocyte, monocyte (NK) , b cell, t cell
• EPCAM for epithelial
• VIM for fibroblasts
• CD31 for endothelial
• CD68 for monocyte

Cluster the cells separately [NOT NEEDED ANYMORE]

• [x] Divide the dataset by epithelial cells and non-epithelial cells. Cluster the two groups separately and try to define the cell type of each cluster.
• [x] Filter epithelial out from the immune-cell dataset; filter immune cells out from epithelial dataset.

cell type decision

• [x] decide the cell type for each cluster
• [ ] Another stream: Use DCA to see if the cells can be separate better.
• [x] Check the cell marker of clusters with the following command pbmc.markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_log2FC) -> top10 DoHeatmap(pbmc, features = top10$gene) + NoLegend()

https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

Sanity check

• [ ] color UMAP by cell cycle
• [x] color UMAP by cell mitochondrial
• [x] by sample
• [x] 10x vs smart-seq
• [x] total RNA

double check:

• [ ] Run another integration (let seurat automatically choose reference)

[XpelC]

Amazing, the only thing left is to give the specific cluster identities. Tomorrow after you have done that we should meet.

I suggest to use SingleR on your clusters for a final confirmation.

Sperm cells are mixed with T cell clusters (cluster 23). Should I label the cluster as sperm or T cell?

[stemangiola]

Amazing, the only thing left is to give the specific cluster identities. Tomorrow after you have done that we should meet. I suggest to use SingleR on your clusters for a final confirmation.

Sperm cells are mixed with T cell clusters (cluster 23). Should I label the cluster as sperm or T cell?

Forget about pserm, we will drop them from the dataset.

For epithelial, just divide them in luminal and basal. There must be markers for that.

[XpelC]

divide them in luminal and basal.

I'll search for it.

[stemangiola]

• Color the umap by cancer and normal sample.

Also it's important to do this

[XpelC]

• FeaturePlot: Use the original umap (split by cell marker, and sample).
• Use features and the markers:

The marker for basal cell (KRT 17)

Also please refer to the original data (the basal cell is found in cluster 4,6,9,16)

[stemangiola]

Great, any marker of luminal?

[XpelC]

Great, any marker of luminal?

If we treat luminal as epithelial, then EPCAM for luminal, KRT17 for basal

[stemangiola]

If we treat luminal as epithelial, then EPCAM for luminal

Fair enough. Let me know when do you want to meet. Please before also complete the colouring by benign/cancer sampels.

[XpelC]

Fair enough. Let me know when do you want to meet. Please before also complete the colouring by benign/cancer sampels.

I'll work on it now

[XpelC]

Fair enough. Let me know when do you want to meet. Please before also complete the colouring by benign/cancer sampels.

tumor vs normal sample. If it is possible, let's meet at 14:00.

[stemangiola]

reference =celldex::MonacoImmuneData()

counts |>
    as.SingleCellExperiment() |>

    # Annotate
    logNormCounts(assay.type = "X") |>

    SingleR(
        ref = monocyte_reference,
        assay.type.test=1,
        labels = reference$label.fine
    )

[stemangiola]

Please provide the seurat object with the macrocluster column in the metadata into the GP_tranfer

1) create a directory in /stornext/General/scratch/GP_Transfer/ 2) copy the seurat object into that directory

[XpelC]

Please provide the seurat object with the macrocluster column in the metadata into the GP_tranfer

done dir: /stornext/General/scratch/GP_Transfer/xinpu_chen

[stemangiola]

Please provide the seurat object with the macrocluster column in the metadata into the GP_tranfer

done dir: /stornext/General/scratch/GP_Transfer/xinpu_chen

Thanks @XpelC ,

I noticed you did not label all the macrocluster we discussed

integrated_sample_annotated |> distinct(macrocluster)

# A tibble: 5 × 1
  macrocluster
  <chr>       
1 epithelial  
2 endothelial 
3 fibroblast  
4 other       
5 T        

Please modify referring to this (we should have 7 macroclusters as we have 7 circles in the image)

[XpelC]

Please modify referring to this (we should have 7 macroclusters as we have 7 circles in the image)

done

[stemangiola]

Please modify referring to this (we should have 7 macroclusters as we have 7 circles in the image)

done

The file

/stornext/General/scratch/GP_Transfer/xinpu_chen/integrated_sample.rds

seems to be unchanged.

Could you please give me the path of your seurat object and execute this on your own file

integrated_sample_annotated <- readRDS("integrated_sample_annotated.rds")

integrated_sample_annotated |> 
  distinct(macrocluster)

[XpelC]

Could you please give me the path of your seurat object and execute this on your own file

path: /stornext/General/scratch/GP_Transfer/xinpu_chen/integrated_sample.rds This time it should work.

[stemangiola]

Hello Xinpu,

the macro cluster distribution seems a bit off, can you confirm that you meant this subdivision?

[XpelC]

the macro cluster distribution seems a bit off, can you confirm that you meant this subdivision?

This part has been fixed

[stemangiola]

Thanks, that's not the only problematic part. Also epithelial are shared between two macroclusters.

[XpelC]

I think I’m able to annotate the immune cell. I’ll look through the epithelial dataset and let you know shortly.

Best wishes, Xinpu

On Sep 21, 2022, at 9:59 AM, Stefano Mangiola @.**@.>> wrote:

Great

other_ cell

Are you able to annotate Immune clusters?

epithelial

Would you be able to color by

• cancer/benign
• luminal/basal

— Reply to this email directly, view it on GitHubhttps://github.com/stemangiola/cellsig/issues/69#issuecomment-1253031845, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALBA442DONM7VMMNX2I4IXTV7JFVLANCNFSM6AAAAAAQK6OQTQ. You are receiving this because you were mentioned.Message ID: @.***>

[stemangiola]

Thanks, please send back the fixed macrocluster UMAP first. We want to do step by step, to not redo any work. Please reply to this message with the UMAP image.

Thanks.

[XpelC]

Thanks, please send back the fixed macrocluster UMAP first. We want to do step by step, to not redo any work. Please reply to this message with the UMAP image.

[XpelC]

reference =celldex::MonacoImmuneData()

The singleR result. Should I left join it with the cell UMI in the original seurat object?

[stemangiola]

reference =celldex::MonacoImmuneData()

The singleR result. Should I left join it with the cell UMI in the original seurat object?

Yes, this is an evidence that you should match with manual curation. Automatic classification is not perfect but helps.

You can choose between: going on the manual curation, or integrate the other datasets that we collected first.

[XpelC]

singleR result

[XpelC]

singleR result.

I'll try to produce macroclusters basing on the singleR result now.

[XpelC]

cell type name formatting The umap of the new integrated data

The umap of separated datasets

new cell types in each cluster seurat_clusters cell_type n

1 0 basal cell of prostate epithelium 36936 2 0 epithelial cell of urethra 10682 3 0 prostate gland microvascular endothelial cell 7990 4 0 secretory cell 5288 5 0 fibroblast of connective tissue of nonglandular part of prostate 4942 6 0 luminal cell of prostate epithelium 4322 7 0 CD1c-positive myeloid dendritic cell 4099 8 0 dendritic cell 3645 9 0 effector CD8-positive, alpha-beta T cell 3551 10 0 B cell 3254 11 0 granulocyte 3105 12 0 smooth muscle cell of prostate 2994 13 0 pericyte cell 2619 14 0 CD4-positive, alpha-beta thymocyte 2471 15 0 epithelial cell 1646 16 0 fibroblast of connective tissue of glandular part of prostate 1640 17 0 vascular associated smooth muscle cell 1602 18 0 basal epithelial cell of prostatic duct 1588 19 0 effector CD4-positive, alpha-beta T cell 1143 20 0 epithelial cell of prostate 1129 21 0 endothelial cell of vascular tree 579 22 0 classical monocyte 375 23 0 skin fibroblast 333 24 0 non-classical monocyte 304 25 0 Luminal 297 26 0 club cell 258 27 0 macrophage 211 28 0 CD141-positive myeloid dendritic cell 199 29 0 T cell 190 30 0 CD8-positive, alpha-beta thymocyte 159 31 0 endocrine cell 152 32 0 mature NK T cell 144 33 0 natural killer cell 132 34 0 Epithelial cell 108 35 0 myeloid cell 73 36 0 Epi_Basal_hillock 70 37 0 CD8-positive, alpha-beta T cell 60 38 0 neutrophil 59 39 0 contractile cell 58 40 0 endothelial cell of lymphatic vessel 57 41 0 Basal 53 42 0 Epi_Luminal_1 49 43 0 Epi_Basal_1 41 44 1 basal cell of prostate epithelium 14501 45 1 Epi_Basal_hillock 8721 46 1 Basal 7124 47 1 epithelial cell of urethra 3070 48 1 Hillock 1987 49 1 Cancer/Epithelial 1920 50 1 Epithelial_cells 1687 51 1 NA 1420 52 1 Epi_Basal_1 1272 53 1 Epithelial cell 754 54 1 Epi_Luminal_2 682 55 1 Basal/intermediate 467 56 1 Luminal 425 57 1 BE 378 58 1 luminal cell of prostate epithelium 370 59 1 secretory cell 351 60 1 basal epithelial cell of prostatic duct 199 61 1 epithelial cell 172 62 1 Epi_Luminal_1 121 63 1 epithelial cell of prostate 114 64 1 smooth muscle cell of prostate 113 65 1 HE 105 66 1 prostate gland microvascular endothelial cell 96 67 1 effector CD8-positive, alpha-beta T cell 82 68 1 fibroblast of connective tissue of prostate 78 69 1 B cell 61 70 1 endothelial cell of vascular tree 60 71 1 pericyte cell 60 72 1 CD4-positive, alpha-beta thymocyte 57 73 1 CE 55 74 1 CD1c-positive myeloid dendritic cell 49 75 1 fibroblast of connective tissue of nonglandular part of prostate 41 76 1 LE-KLK4 38 77 1 club cell 38 78 1 T cell 36 79 1 CD8-positive, alpha-beta T cell 31 80 2 basal cell of prostate epithelium 13965 81 2 epithelial cell of urethra 2432 82 2 luminal cell of prostate epithelium 2161 83 2 CD1c-positive myeloid dendritic cell 1815 84 2 Basal 1590 85 2 dendritic cell 1217 86 2 prostate gland microvascular endothelial cell 1166 87 2 Luminal 1101 88 2 fibroblast of connective tissue of nonglandular part of prostate 985 89 2 epithelial cell 972 90 2 secretory cell 954 91 2 smooth muscle cell of prostate 922 92 2 effector CD8-positive, alpha-beta T cell 846 93 2 Epithelial cell 833 94 2 pericyte cell 773 95 2 basal epithelial cell of prostatic duct 759 96 2 Sperm 744 97 2 B cell 665 98 2 fibroblast of connective tissue of glandular part of prostate 654 99 2 Epi_Basal_hillock 604 100 2 LE-KLK4 496 101 2 fibroblast of connective tissue of prostate 489 102 2 epithelial cell of prostate 478 103 2 granulocyte 475 104 2 vascular associated smooth muscle cell 470 105 2 T cell 414 106 2 endocrine cell 407 107 2 CD4-positive, alpha-beta thymocyte 382 108 2 club cell 372 109 2 CD8-positive, alpha-beta T cell 273 110 2 effector CD4-positive, alpha-beta T cell 248 111 2 Endothelial 232 112 2 endothelial cell of vascular tree 223 113 2 endothelial cell 212 114 2 Str_VascEndo_1 179 115 2 mature NK T cell 173 116 2 Epi_Basal_1 169 117 2 Epi_Luminal_2 164 118 2 Epi_Luminal_1 152 119 2 Str_Lymph_Endo 140 120 2 classical monocyte 130 121 2 smooth muscle cell 115 122 2 macrophage 113 123 2 Hillock 108 124 2 Endothelial_cells 106 125 2 myeloid cell 104 126 2 skin fibroblast 100 127 2 non-classical monocyte 95 128 2 fibroblast 85 129 2 Endothelia 75 130 2 NA 72 131 2 CD141-positive myeloid dendritic cell 60 132 2 Str_VascEndo_2 59 133 2 Epithelial_cells 50 134 2 basal cell 49 135 2 endothelial cell of lymphatic vessel 42 136 2 natural killer cell 39 137 2 CD8-positive, alpha-beta thymocyte 31 138 3 basal cell of prostate epithelium 26381 139 3 luminal cell of prostate epithelium 3892 140 3 secretory cell 3633 141 3 epithelial cell of urethra 1448 142 3 prostate gland microvascular endothelial cell 1272 143 3 fibroblast of connective tissue of prostate 1124 144 3 smooth muscle cell of prostate 1080 145 3 leukocyte 383 146 3 basal epithelial cell of prostatic duct 318 147 3 Luminal 311 148 3 endothelial cell of vascular tree 254 149 3 epithelial cell of prostate 234 150 3 Epithelial cell 192 151 3 Basal 110 152 3 macrophage 92 153 3 epithelial cell 75 154 3 T cell 72 155 3 Epi_Basal_hillock 67 156 3 Epi_Luminal_1 67 157 3 B cell 47 158 3 skin fibroblast 42 159 3 Epi_Basal_1 37 160 4 Luminal 9395 161 4 Epithelial_cells 4521 162 4 Epithelial cell 4463 163 4 basal cell of prostate epithelium 3773 164 4 Epi_Luminal_1 2698 165 4 luminal cell of prostate epithelium 2608 166 4 NA 1800 167 4 LE-KLK3 1541 168 4 Basal 1269 169 4 LE-KLK4 1119 170 4 Epi_Basal_hillock 901 171 4 Cancer/Epithelial 829 172 4 epithelial cell of urethra 542 173 4 Epi_Luminal_2 483 174 4 secretory cell 236 175 4 Hillock 195 176 4 basal epithelial cell of prostatic duct 93 177 4 epithelial cell 91 178 4 Epi_Basal_1 78 179 4 fibroblast of connective tissue of prostate 77 180 4 B cell 61 181 4 Sperm 61 182 4 prostate gland microvascular endothelial cell 61 183 4 smooth muscle cell of prostate 60 184 4 Club 57 185 4 CE 52 186 4 epithelial cell of prostate 49 187 4 Basal/intermediate 40 188 4 neuroendocrine cell 40 189 5 basal cell of prostate epithelium 7109 190 5 Basal 4210 191 5 Luminal 3857 192 5 Epithelial_cells 2188 193 5 Epithelial cell 1831 194 5 LE-KLK4 1506 195 5 luminal cell of prostate epithelium 1073 196 5 Epi_Luminal_1 922 197 5 NA 607 198 5 LE-KLK3 606 199 5 epithelial cell of urethra 544 200 5 Epi_Basal_1 539 201 5 B cell 490 202 5 Epi_Basal_hillock 441 203 5 epithelial cell 392 204 5 basal epithelial cell of prostatic duct 382 205 5 granulocyte 346 206 5 Cancer/Epithelial 345 207 5 Sperm 193 208 5 Mast 192 209 5 CD4-positive, alpha-beta thymocyte 188 210 5 secretory cell 188 211 5 Imm_T_CD4 170 212 5 fibroblast of connective tissue of prostate 157 213 5 epithelial cell of prostate 137 214 5 Epi_Luminal_2 136 215 5 T cell 129 216 5 Hillock 121 217 5 smooth muscle cell of prostate 119 218 5 vascular associated smooth muscle cell 111 219 5 effector CD8-positive, alpha-beta T cell 109 220 5 fibroblast of connective tissue of nonglandular part of prostate 107 221 5 club cell 104 222 5 prostate gland microvascular endothelial cell 97 223 5 effector CD4-positive, alpha-beta T cell 92 224 5 Fibroblast 87 225 5 Endothelial 86 226 5 Basal/intermediate 84 227 5 Str_VascEndo_1 79 228 5 Str_Mes_1 75 229 5 endothelial cell of vascular tree 75 230 5 pericyte cell 72 231 5 endocrine cell 71 232 5 Imm_T_CD8 68 233 5 Str_Glial 59 234 5 endothelial cell 57 235 5 fibroblast of connective tissue of glandular part of prostate 49 236 5 CD8-positive, alpha-beta T cell 45 237 5 Club 44 238 5 CE 43 239 5 CD1c-positive myeloid dendritic cell 37 240 5 skin fibroblast 37 241 5 T 36 242 5 Str_Lymph_Endo 34 243 6 Luminal 6954 244 6 basal cell of prostate epithelium 3695 245 6 Basal 2848 246 6 Epithelial cell 2461 247 6 Epithelial_cells 1962 248 6 Epi_Luminal_1 1685 249 6 luminal cell of prostate epithelium 860 250 6 NA 705 251 6 Cancer/Epithelial 679 252 6 LE-KLK3 421 253 6 epithelial cell of urethra 276 254 6 Epi_Basal_hillock 245 255 6 CE 220 256 6 Epi_Luminal_2 202 257 6 Epi_Basal_1 189 258 6 basal epithelial cell of prostatic duct 154 259 6 epithelial cell 129 260 6 secretory cell 107 261 6 Hillock 84 262 6 LE-KLK4 80 263 6 T cell 79 264 6 B cell 77 265 6 Sperm 70 266 6 epithelial cell of prostate 60 267 6 Club 53 268 6 smooth muscle cell of prostate 48 269 6 granulocyte 43 270 6 mast cell 39 271 6 Basal/intermediate 38 272 6 Endothelial 37 273 6 Mast 32 274 7 Epi_Luminal_2 6478 275 7 secretory cell 3565 276 7 basal cell of prostate epithelium 2476 277 7 Club 1263 278 7 Epi_Luminal_1 1045 279 7 Epithelial cell 1006 280 7 epithelial cell of urethra 969 281 7 Epithelial_cells 891 282 7 CE 818 283 7 Basal 739 284 7 luminal cell of prostate epithelium 683 285 7 Hillock 655 286 7 Cancer/Epithelial 555 287 7 Luminal 533 288 7 Basal/intermediate 379 289 7 NA 327 290 7 epithelial cell 208 291 7 Epi_Basal_hillock 159 292 7 basal epithelial cell of prostatic duct 109 293 7 effector CD8-positive, alpha-beta T cell 99 294 7 fibroblast of connective tissue of nonglandular part of prostate 90 295 7 smooth muscle cell of prostate 82 296 7 prostate gland microvascular endothelial cell 67 297 7 B cell 66 298 7 epithelial cell of prostate 62 299 7 CD4-positive, alpha-beta thymocyte 61 300 7 LE-KLK4 55 301 7 T cell 49 302 7 CD1c-positive myeloid dendritic cell 41 303 7 club cell 40 304 7 endothelial cell of vascular tree 39 305 7 pericyte cell 39 306 7 effector CD4-positive, alpha-beta T cell 38 307 7 endocrine cell 38 308 7 CD8-positive, alpha-beta T cell 33 309 7 fibroblast of connective tissue of prostate 32 310 8 basal cell of prostate epithelium 5348 311 8 luminal cell of prostate epithelium 1365 312 8 Basal 917 313 8 epithelial cell of urethra 799 314 8 basal epithelial cell of prostatic duct 616 315 8 prostate gland microvascular endothelial cell 600 316 8 epithelial cell 462 317 8 B cell 431 318 8 T 416 319 8 epithelial cell of prostate 363 320 8 smooth muscle cell of prostate 343 321 8 effector CD8-positive, alpha-beta T cell 307 322 8 Epi_Basal_hillock 305 323 8 Imm_Plasma 263 324 8 fibroblast of connective tissue of nonglandular part of prostate 244 325 8 T cell 238 326 8 Luminal 236 327 8 Mast 231 328 8 secretory cell 212 329 8 pericyte cell 202 330 8 Monocyte 201 331 8 CD8-positive, alpha-beta thymocyte 200 332 8 club cell 190 333 8 CD4-positive, alpha-beta thymocyte 187 334 8 CD1c-positive myeloid dendritic cell 186 335 8 dendritic cell 183 336 8 natural killer cell 178 337 8 endocrine cell 157 338 8 Epithelial cell 154 339 8 leukocyte 141 340 8 endothelial cell of vascular tree 138 341 8 Imm_B 119 342 8 Hillock 108 343 8 macrophage 104 344 8 fibroblast of connective tissue of prostate 103 345 8 effector CD4-positive, alpha-beta T cell 101 346 8 fibroblast of connective tissue of glandular part of prostate 101 347 8 Pre-B_cell_CD34- 99 348 8 Myeloid 94 349 8 granulocyte 91 350 8 skin fibroblast 91 351 8 Epi_Basal_1 88 352 8 Epi_Luminal_1 85 353 8 Sperm 84 354 8 Epi_Luminal_2 77 355 8 Imm_T_CD4 66 356 8 LE-KLK4 66 357 8 Plasma cells 65 358 8 myeloid cell 60 359 8 Mac1 55 360 8 CD8-positive, alpha-beta T cell 51 361 8 mature NK T cell 51 362 8 vascular associated smooth muscle cell 51 363 8 Epithelial_cells 48 364 8 NA 48 365 8 DC 45 366 8 Monocytes/Macrophages 39 367 8 Monocytes 37 368 8 endothelial cell 33 369 8 Fibroblast 32 370 8 Imm_NK 32 371 8 Monocytic 31 372 9 T cell 3795 373 9 T 2763 374 9 CD8+ Tem 1938 375 9 Imm_T_CD8 1786 376 9 Imm_T_CD4 1691 377 9 T-cells 671 378 9 Mast 497 379 9 NA 484 380 9 Imm_T_IFNG 454 381 9 CD8 Trm 449 382 9 basal cell of prostate epithelium 434 383 9 NK_cell 316 384 9 CD4 naive-cm 211 385 9 CD4 Trm 152 386 9 leukocyte 151 387 9 CD8 cytotoxic 129 388 9 Treg 107 389 9 Luminal 85 390 9 NK cell 78 391 9 Leukocytes 77 392 9 NK cells 73 393 9 luminal cell of prostate epithelium 67 394 9 Epithelial cell 65 395 9 Monocytic 65 396 9 NK CD16pos 60 397 9 B cell 57 398 9 Basal 49 399 9 Epithelial_cells 49 400 9 NK CD16neg 45 401 9 epithelial cell of urethra 41 402 9 secretory cell 35 403 9 Endothelial 34 404 9 Monocyte 31 405 10 basal cell of prostate epithelium 2580 406 10 Fibroblast 1108 407 10 Smooth muscle 1077 408 10 Basal 822 409 10 PVL cells 803 410 10 Endothelial 763 411 10 Str_Mes_2 715 412 10 smooth muscle cell of prostate 701 413 10 Apidocytes 531 414 10 luminal cell of prostate epithelium 503 415 10 Str_SM 502 416 10 epithelial cell of urethra 502 417 10 Myofibroblast 422 418 10 B cell 382 419 10 basal epithelial cell of prostatic duct 264 420 10 endothelial cell of vascular tree 241 421 10 fibroblast of connective tissue of nonglandular part of prostate 225 422 10 epithelial cell 216 423 10 epithelial cell of prostate 182 424 10 Epi_Basal_hillock 165 425 10 CD1c-positive myeloid dendritic cell 144 426 10 secretory cell 136 427 10 Luminal 113 428 10 dendritic cell 92 429 10 Str_SM_myofibro 82 430 10 Epithelial cell 81 431 10 CD4-positive, alpha-beta thymocyte 79 432 10 prostate gland microvascular endothelial cell 70 433 10 fibroblast of connective tissue of prostate 66 434 10 fibroblast of connective tissue of glandular part of prostate 56 435 10 endocrine cell 55 436 10 Epithelial_cells 49 437 10 Sperm 47 438 10 effector CD4-positive, alpha-beta T cell 45 439 10 effector CD8-positive, alpha-beta T cell 44 440 10 T cell 43 441 10 club cell 42 442 10 Str_Mes_1 39 443 10 granulocyte 38 444 10 Epi_Basal_1 36 445 10 CD8-positive, alpha-beta T cell 33 446 10 Mast 31 447 11 basal cell of prostate epithelium 2705 448 11 Fibroblast 2661 449 11 Str_Mes_1 1622 450 11 Smooth_muscle_cells 602 451 11 prostate stromal cell 557 452 11 luminal cell of prostate epithelium 513 453 11 CAFs 401 454 11 epithelial cell of urethra 307 455 11 Basal 286 456 11 basal epithelial cell of prostatic duct 274 457 11 fibroblast of connective tissue of prostate 262 458 11 Str_SM_myofibro 247 459 11 epithelial cell 216 460 11 prostate gland microvascular endothelial cell 189 461 11 epithelial cell of prostate 181 462 11 fibroblast of connective tissue of nonglandular part of prostate 174 463 11 Mast 163 464 11 smooth muscle cell of prostate 154 465 11 endothelial cell of vascular tree 134 466 11 effector CD8-positive, alpha-beta T cell 109 467 11 secretory cell 103 468 11 CD1c-positive myeloid dendritic cell 100 469 11 Epi_Basal_hillock 95 470 11 endocrine cell 83 471 11 fibroblast of connective tissue of glandular part of prostate 81 472 11 pericyte cell 77 473 11 Str_Glial 76 474 11 Unassigned 76 475 11 dendritic cell 75 476 11 Luminal 73 477 11 B cell 64 478 11 granulocyte 64 479 11 club cell 62 480 11 T cell 61 481 11 CD4-positive, alpha-beta thymocyte 60 482 11 skin fibroblast 50 483 11 Epithelial cell 48 484 11 CD8-positive, alpha-beta T cell 47 485 11 Epi_Basal_1 41 486 11 LE-KLK4 40 487 11 Epithelial_cells 39 488 11 vascular associated smooth muscle cell 39 489 11 endothelial cell 36 490 11 Sperm 35 491 11 effector CD4-positive, alpha-beta T cell 32 492 12 Endothelial 4166 493 12 Str_VascEndo_1 3361 494 12 Endothelia 1505 495 12 Endothelial_cells 1044 496 12 prostate gland microvascular endothelial cell 1018 497 12 Endothelial cell 704 498 12 Str_Lymph_Endo 675 499 12 basal cell of prostate epithelium 137 500 12 Str_VascEndo_2 112 501 12 Fibroblast 104 502 12 NA 98 503 12 Mast 79 504 12 Luminal 54 505 12 T 39 506 12 smooth muscle cell of prostate 32 507 13 basal cell of prostate epithelium 4030 508 13 luminal cell of prostate epithelium 1197 509 13 Basal 616 510 13 epithelial cell of urethra 588 511 13 epithelial cell 380 512 13 effector CD8-positive, alpha-beta T cell 335 513 13 basal epithelial cell of prostatic duct 321 514 13 prostate gland microvascular endothelial cell 314 515 13 CD4-positive, alpha-beta thymocyte 251 516 13 Epithelial cell 234 517 13 Luminal 232 518 13 secretory cell 225 519 13 T cell 217 520 13 fibroblast of connective tissue of nonglandular part of prostate 211 521 13 effector CD4-positive, alpha-beta T cell 207 522 13 B cell 196 523 13 smooth muscle cell of prostate 187 524 13 epithelial cell of prostate 186 525 13 Imm_T_CD8 185 526 13 CD1c-positive myeloid dendritic cell 176 527 13 granulocyte 161 528 13 Imm_T_CD4 152 529 13 dendritic cell 123 530 13 endothelial cell of vascular tree 109 531 13 fibroblast of connective tissue of prostate 109 532 13 endocrine cell 108 533 13 pericyte cell 108 534 13 vascular associated smooth muscle cell 107 535 13 Sperm 105 536 13 fibroblast of connective tissue of glandular part of prostate 100 537 13 club cell 93 538 13 T 80 539 13 Epi_Basal_hillock 75 540 13 CD8-positive, alpha-beta T cell 70 541 13 Epithelial_cells 67 542 13 LE-KLK4 58 543 13 Epi_Basal_1 48 544 13 CD8+ Tem 45 545 13 endothelial cell 45 546 13 macrophage 43 547 13 Epi_Luminal_2 42 548 13 Epi_Luminal_1 40 549 13 mature NK T cell 40 550 13 skin fibroblast 40 551 13 Mast 37 552 13 Hillock 32 553 14 Monocyte 1624 554 14 Monocytic 1142 555 14 leukocyte 846 556 14 Myeloid 814 557 14 NA 521 558 14 T 280 559 14 Macrophage 272 560 14 Leukocytes 266 561 14 Monocytes 207 562 14 Imm_Myeloid 173 563 14 Monocytes/Macrophages 152 564 14 Endothelial 123 565 14 Imm_DC 86 566 14 Mast 76 567 14 Mac1 75 568 14 basal cell of prostate epithelium 74 569 14 Luminal 66 570 14 Mono 60 571 14 B cell 53 572 14 Mac2 44 573 14 DC 42 574 15 luminal cell of prostate epithelium 2935 575 15 basal epithelial cell of prostatic duct 924 576 15 epithelial cell of prostate 269 577 15 smooth muscle cell of prostate 263 578 15 epithelial cell 231 579 15 endothelial cell of vascular tree 207 580 15 macrophage 167 581 15 basal cell of prostate epithelium 131 582 15 skin fibroblast 99 583 15 contractile cell 37 584 16 luminal cell of prostate epithelium 1813 585 16 basal epithelial cell of prostatic duct 906 586 16 epithelial cell of prostate 828 587 16 endothelial cell of vascular tree 264 588 16 epithelial cell 221 589 16 skin fibroblast 175 590 16 smooth muscle cell of prostate 173 591 16 T cell 113 592 16 basal cell of prostate epithelium 87 593 16 macrophage 87 594 16 neutrophil 33 595 17 mast cell 882 596 17 Mast 613 597 17 Imm_NK 390 598 17 basal cell of prostate epithelium 229 599 17 Epithelial_cells 215 600 17 MAST cells 68 601 17 T 38 602 29 luminal cell of prostate epithelium 111 603 29 basal epithelial cell of prostatic duct 71 604 29 epithelial cell of prostate 53 605 29 basal cell of prostate epithelium 52 606 29 endothelial cell of vascular tree 42 607 29 Luminal 38 608 29 smooth muscle cell of prostate 38 609 29 epithelial cell 33