First explorative tasks

stemangiola commented 2 years ago

We have 4 parsed Seurat datasets with the columns (if you use tidyseurat you can see this)

.cell, sample, dataset, cell_type

Get a table of total cell number per sample per dataset (print out a tibble)
Get unique cell type lists for each dataset (print out a tibble, seurat_obj |> distinct(dataset, sample, cell_type))
Create pseudobulk for each sample and visualise all samples in a principal component plot (what's the variability within dataset compared to across dataset)
Create pseudobulk for each sample/cell_type and visualise all samples in a principal component plot (what's the variability within dataset compared to across dataset and cell types)
For each dataset separately, integrate the samples (if needed) and draw UMAP plots (dataset heterogeneity at the single-cell level)

XpelC commented 2 years ago

Get a table of total cell number per sample per dataset (print out a tibble)

# A tibble: 51 × 3
   dataset         sample                             n
   <chr>           <chr>                          <int>
 1 EGAS00001005115 " M-P1"                        10224
 2 EGAS00001005115 "BC-P1"                        11115
 3 EGAS00001005115 "BC-P2"                        11763
 4 EGAS00001005115 "BC-P3"                         7154
 5 EGAS00001005115 "PC-P1"                         8723
 6 EGAS00001005787 "SLX-15732SIGAC4HTVNWBBXXs_6"   1887
 7 EGAS00001005787 "SLX-15732SIGAD4HTVNWBBXXs_6"   2687
 8 EGAS00001005787 "SLX-15736SIGAA9HTHM2BBXXs_4"    838
 9 EGAS00001005787 "SLX-15736SIGAA9HTHM2BBXXs_5"    841
10 EGAS00001005787 "SLX-15736SIGAB9HTHM2BBXXs_4"   1064
11 EGAS00001005787 "SLX-15736SIGAB9HTHM2BBXXs_5"   1056
12 EGAS00001005787 "SLX-15736SIGAD8HTHM2BBXXs_4"    857
13 EGAS00001005787 "SLX-15736SIGAD8HTHM2BBXXs_5"    844
14 EGAS00001005787 "SLX-15736SIGAE8HTHM2BBXXs_4"    250
15 EGAS00001005787 "SLX-15736SIGAE8HTHM2BBXXs_5"    244
16 EGAS00001005787 "SLX-15929SIGAC4HVLYKBBXXs_8"   1099
17 EGAS00001005787 "SLX-15929SIGAD4HVLYKBBXXs_8"    111
18 EGAS00001005787 "SLX-15929SIGAG11HVLYKBBXXs_8"    88
19 EGAS00001005787 "SLX-15929SIGAH11HVLYKBBXXs_8"   103
20 EGAS00001005787 "SLX-16140SIGAB1HVMFKBBXXs_3"    148
21 EGAS00001005787 "SLX-16140SIGAC1HVMFKBBXXs_3"    858
22 EGAS00001005787 "SLX-16142SIGAG6HVMFKBBXXs_4"    699
23 EGAS00001005787 "SLX-16142SIGAH6HVMFKBBXXs_4"   1136
24 EGAS00001005787 "SLX-16147SIGAE7HVMFKBBXXs_7"    486
25 EGAS00001005787 "SLX-16147SIGAF7HVMFKBBXXs_7"    613
26 EGAS00001005787 "SLX-16148SIGAG7HVMFKBBXXs_8"    221
27 EGAS00001005787 "SLX-16148SIGAH7HVMFKBBXXs_8"     91
28 EGAS00001005787 "SLX-16362SIGAA3HWFTVBBXXs_4"    692
29 EGAS00001005787 "SLX-16362SIGAB3HWFTVBBXXs_4"    195
30 GSE137829       "GSM4089151"                    3022
31 GSE137829       "GSM4089152"                     950
32 GSE137829       "GSM4089153"                     965
33 GSE137829       "GSM4089154"                    1062
34 GSE137829       "GSM4711414"                    8690
35 GSE137829       "GSM4711415"                    6603
36 GSE141445       "GSM4203181"                   36424
37 GSE176031       "AUG_PB1"                        933
38 GSE176031       "MAY_PB1"                       3568
39 GSE176031       "MAY_PB2"                       2135
40 GSE176031       "PR5186"                         763
41 GSE176031       "PR5196"                        1993
42 GSE176031       "PR5199"                        1025
43 GSE176031       "PR5249_N"                      1683
44 GSE176031       "PR5249_T"                       810
45 GSE176031       "PR5251_N"                      1135
46 GSE176031       "PR5251_T"                      1830
47 GSE176031       "PR5254_N"                       980
48 GSE176031       "PR5254_T"                       493
49 GSE176031       "PR5261_N"                       934
50 GSE176031       "PR5261_T"                      1561
51 GSE176031       "PR5269"                        1900

Get unique cell type lists for each dataset (print out a tibble, seurat_obj |> distinct(dataset, sample, cell_type))

# A tibble: 652 × 3
    sample                         cell_type                     dataset        
    <chr>                          <chr>                         <chr>          
  1 "BC-P1"                        Endothelial                   EGAS00001005115
  2 "BC-P1"                        Cancer/Epithelial             EGAS00001005115
  3 "BC-P1"                        Monocytes/Macrophages         EGAS00001005115
  4 "BC-P1"                        PVL cells                     EGAS00001005115
  5 "BC-P1"                        CAFs                          EGAS00001005115
  6 "BC-P1"                        Cancer/Epithelial Cycling     EGAS00001005115
  7 "BC-P1"                        T-cells                       EGAS00001005115
  8 "BC-P1"                        Plasmablasts                  EGAS00001005115
  9 "BC-P1"                        B-cells                       EGAS00001005115
 10 "BC-P1"                        Myoepithelial                 EGAS00001005115
 11 "BC-P2"                        T-cells                       EGAS00001005115
 12 "BC-P2"                        Cancer/Epithelial             EGAS00001005115
 13 "BC-P2"                        Doublets                      EGAS00001005115
 14 "BC-P2"                        B-cells                       EGAS00001005115
 15 "BC-P2"                        Myoepithelial                 EGAS00001005115
 16 "BC-P2"                        Endothelial                   EGAS00001005115
 17 "BC-P2"                        T-cells Cycling               EGAS00001005115
 18 "BC-P2"                        Mouse 3T3 spike-in            EGAS00001005115
 19 "BC-P2"                        Unassigned                    EGAS00001005115
 20 "BC-P2"                        PVL cells                     EGAS00001005115
 21 "BC-P2"                        pDCs                          EGAS00001005115
 22 "BC-P2"                        Plasmablasts                  EGAS00001005115
 23 "BC-P2"                        Monocytes/Macrophages         EGAS00001005115
 24 "BC-P2"                        CAFs                          EGAS00001005115
 25 "BC-P3"                        Monocytes/Macrophages Cycling EGAS00001005115
 26 "BC-P3"                        T-cells                       EGAS00001005115
 27 "BC-P3"                        Cancer/Epithelial             EGAS00001005115
 28 "BC-P3"                        Monocytes/Macrophages         EGAS00001005115
 29 "BC-P3"                        T-cells Cycling               EGAS00001005115
 30 "BC-P3"                        PVL cells                     EGAS00001005115
 31 "BC-P3"                        cDCs                          EGAS00001005115
 32 "BC-P3"                        Endothelial                   EGAS00001005115
 33 "BC-P3"                        Unassigned                    EGAS00001005115
 34 "BC-P3"                        CAFs                          EGAS00001005115
 35 "BC-P3"                        Plasmablasts                  EGAS00001005115
 36 "PC-P1"                        Cancer/Epithelial             EGAS00001005115
 37 "PC-P1"                        Endothelial                   EGAS00001005115
 38 "PC-P1"                        CAFs                          EGAS00001005115
 39 "PC-P1"                        Monocytes/Macrophages         EGAS00001005115
 40 "PC-P1"                        PVL cells                     EGAS00001005115
 41 "PC-P1"                        NK cells                      EGAS00001005115
 42 "PC-P1"                        Unassigned                    EGAS00001005115
 43 "PC-P1"                        MAST cells                    EGAS00001005115
 44 "PC-P1"                        T-cells                       EGAS00001005115
 45 "PC-P1"                        Cancer/Epithelial Cycling     EGAS00001005115
 46 "PC-P1"                        B-cells                       EGAS00001005115
 47 " M-P1"                        Cancer                        EGAS00001005115
 48 " M-P1"                        Monocytes/Macrophages         EGAS00001005115
 49 " M-P1"                        T-cells                       EGAS00001005115
 50 " M-P1"                        B-cells                       EGAS00001005115
 51 " M-P1"                        CAFs                          EGAS00001005115
 52 " M-P1"                        Endothelial 1                 EGAS00001005115
 53 " M-P1"                        Endothelial 2                 EGAS00001005115
 54 " M-P1"                        Plasmablasts                  EGAS00001005115
 55 " M-P1"                        pDCs                          EGAS00001005115
 56 "SLX-15732SIGAC4HTVNWBBXXs_6"  T cell                        EGAS00001005787
 57 "SLX-15732SIGAC4HTVNWBBXXs_6"  Mac1                          EGAS00001005787
 58 "SLX-15732SIGAC4HTVNWBBXXs_6"  Endothelial                   EGAS00001005787
 59 "SLX-15732SIGAC4HTVNWBBXXs_6"  LE-KLK3                       EGAS00001005787
 60 "SLX-15732SIGAC4HTVNWBBXXs_6"  DC                            EGAS00001005787
 61 "SLX-15732SIGAC4HTVNWBBXXs_6"  NK cell                       EGAS00001005787
 62 "SLX-15732SIGAC4HTVNWBBXXs_6"  Mono                          EGAS00001005787
 63 "SLX-15732SIGAC4HTVNWBBXXs_6"  Mast cell                     EGAS00001005787
 64 "SLX-15732SIGAC4HTVNWBBXXs_6"  CE                            EGAS00001005787
 65 "SLX-15732SIGAC4HTVNWBBXXs_6"  Mac-MT1                       EGAS00001005787
 66 "SLX-15732SIGAC4HTVNWBBXXs_6"  LE-KLK4                       EGAS00001005787
 67 "SLX-15732SIGAC4HTVNWBBXXs_6"  Sperm                         EGAS00001005787
 68 "SLX-15732SIGAC4HTVNWBBXXs_6"  BE                            EGAS00001005787
 69 "SLX-15732SIGAC4HTVNWBBXXs_6"  Mac2                          EGAS00001005787
 70 "SLX-15732SIGAC4HTVNWBBXXs_6"  HE                            EGAS00001005787
 71 "SLX-15732SIGAC4HTVNWBBXXs_6"  Fibroblast                    EGAS00001005787
 72 "SLX-15732SIGAC4HTVNWBBXXs_6"  B cell                        EGAS00001005787
 73 "SLX-15732SIGAD4HTVNWBBXXs_6"  T cell                        EGAS00001005787
 74 "SLX-15732SIGAD4HTVNWBBXXs_6"  BE                            EGAS00001005787
 75 "SLX-15732SIGAD4HTVNWBBXXs_6"  CE                            EGAS00001005787
 76 "SLX-15732SIGAD4HTVNWBBXXs_6"  LE-KLK3                       EGAS00001005787
 77 "SLX-15732SIGAD4HTVNWBBXXs_6"  Endothelial                   EGAS00001005787
 78 "SLX-15732SIGAD4HTVNWBBXXs_6"  LE-KLK4                       EGAS00001005787
 79 "SLX-15732SIGAD4HTVNWBBXXs_6"  Mac2                          EGAS00001005787
 80 "SLX-15732SIGAD4HTVNWBBXXs_6"  Mac1                          EGAS00001005787
 81 "SLX-15732SIGAD4HTVNWBBXXs_6"  Sperm                         EGAS00001005787
 82 "SLX-15732SIGAD4HTVNWBBXXs_6"  DC                            EGAS00001005787
 83 "SLX-15732SIGAD4HTVNWBBXXs_6"  NK cell                       EGAS00001005787
 84 "SLX-15732SIGAD4HTVNWBBXXs_6"  HE                            EGAS00001005787
 85 "SLX-15732SIGAD4HTVNWBBXXs_6"  B cell                        EGAS00001005787
 86 "SLX-15732SIGAD4HTVNWBBXXs_6"  Fibroblast                    EGAS00001005787
 87 "SLX-15732SIGAD4HTVNWBBXXs_6"  Mast cell                     EGAS00001005787
 88 "SLX-15736SIGAA9HTHM2BBXXs_4"  CD4 naive-cm                  EGAS00001005787
 89 "SLX-15736SIGAA9HTHM2BBXXs_4"  CE                            EGAS00001005787
 90 "SLX-15736SIGAA9HTHM2BBXXs_4"  LE-KLK3                       EGAS00001005787
 91 "SLX-15736SIGAA9HTHM2BBXXs_4"  CD8 cytotoxic                 EGAS00001005787
 92 "SLX-15736SIGAA9HTHM2BBXXs_4"  LE-KLK4                       EGAS00001005787
 93 "SLX-15736SIGAA9HTHM2BBXXs_4"  CD4 Trm                       EGAS00001005787
 94 "SLX-15736SIGAA9HTHM2BBXXs_4"  DC                            EGAS00001005787
 95 "SLX-15736SIGAA9HTHM2BBXXs_4"  NK CD16pos                    EGAS00001005787
 96 "SLX-15736SIGAA9HTHM2BBXXs_4"  BE                            EGAS00001005787
 97 "SLX-15736SIGAA9HTHM2BBXXs_4"  B cell                        EGAS00001005787
 98 "SLX-15736SIGAA9HTHM2BBXXs_4"  Treg                          EGAS00001005787
 99 "SLX-15736SIGAA9HTHM2BBXXs_4"  CD8 Trm                       EGAS00001005787
100 "SLX-15736SIGAA9HTHM2BBXXs_4"  HE                            EGAS00001005787
101 "SLX-15736SIGAA9HTHM2BBXXs_4"  NK CD16neg                    EGAS00001005787
102 "SLX-15736SIGAA9HTHM2BBXXs_4"  Mono                          EGAS00001005787
103 "SLX-15736SIGAA9HTHM2BBXXs_4"  Mac-MT1                       EGAS00001005787
104 "SLX-15736SIGAA9HTHM2BBXXs_4"  Mac1                          EGAS00001005787
105 "SLX-15736SIGAA9HTHM2BBXXs_4"  Mac-cycling                   EGAS00001005787
106 "SLX-15736SIGAA9HTHM2BBXXs_4"  Endothelial                   EGAS00001005787
107 "SLX-15736SIGAA9HTHM2BBXXs_4"  Mast cell                     EGAS00001005787
108 "SLX-15736SIGAA9HTHM2BBXXs_4"  Sperm                         EGAS00001005787
109 "SLX-15736SIGAA9HTHM2BBXXs_5"  CD4 naive-cm                  EGAS00001005787
110 "SLX-15736SIGAA9HTHM2BBXXs_5"  CE                            EGAS00001005787
111 "SLX-15736SIGAA9HTHM2BBXXs_5"  LE-KLK3                       EGAS00001005787
112 "SLX-15736SIGAA9HTHM2BBXXs_5"  CD8 cytotoxic                 EGAS00001005787
113 "SLX-15736SIGAA9HTHM2BBXXs_5"  LE-KLK4                       EGAS00001005787
114 "SLX-15736SIGAA9HTHM2BBXXs_5"  CD4 Trm                       EGAS00001005787
115 "SLX-15736SIGAA9HTHM2BBXXs_5"  DC                            EGAS00001005787
116 "SLX-15736SIGAA9HTHM2BBXXs_5"  NK CD16pos                    EGAS00001005787
117 "SLX-15736SIGAA9HTHM2BBXXs_5"  BE                            EGAS00001005787
118 "SLX-15736SIGAA9HTHM2BBXXs_5"  B cell                        EGAS00001005787
119 "SLX-15736SIGAA9HTHM2BBXXs_5"  Treg                          EGAS00001005787
120 "SLX-15736SIGAA9HTHM2BBXXs_5"  CD8 Trm                       EGAS00001005787
121 "SLX-15736SIGAA9HTHM2BBXXs_5"  HE                            EGAS00001005787
122 "SLX-15736SIGAA9HTHM2BBXXs_5"  NK CD16neg                    EGAS00001005787
123 "SLX-15736SIGAA9HTHM2BBXXs_5"  Mono                          EGAS00001005787
124 "SLX-15736SIGAA9HTHM2BBXXs_5"  Mac-MT1                       EGAS00001005787
125 "SLX-15736SIGAA9HTHM2BBXXs_5"  Mac1                          EGAS00001005787
126 "SLX-15736SIGAA9HTHM2BBXXs_5"  Mac-cycling                   EGAS00001005787
127 "SLX-15736SIGAA9HTHM2BBXXs_5"  Endothelial                   EGAS00001005787
128 "SLX-15736SIGAA9HTHM2BBXXs_5"  Mast cell                     EGAS00001005787
129 "SLX-15736SIGAA9HTHM2BBXXs_5"  Sperm                         EGAS00001005787
130 "SLX-15736SIGAB9HTHM2BBXXs_4"  Sperm                         EGAS00001005787
131 "SLX-15736SIGAB9HTHM2BBXXs_4"  NK CD16neg                    EGAS00001005787
132 "SLX-15736SIGAB9HTHM2BBXXs_4"  LE-KLK3                       EGAS00001005787
133 "SLX-15736SIGAB9HTHM2BBXXs_4"  LE-KLK4                       EGAS00001005787
134 "SLX-15736SIGAB9HTHM2BBXXs_4"  CE                            EGAS00001005787
135 "SLX-15736SIGAB9HTHM2BBXXs_4"  CD8 Trm                       EGAS00001005787
136 "SLX-15736SIGAB9HTHM2BBXXs_4"  CD4 naive-cm                  EGAS00001005787
137 "SLX-15736SIGAB9HTHM2BBXXs_4"  Mac1                          EGAS00001005787
138 "SLX-15736SIGAB9HTHM2BBXXs_4"  CD4 Trm                       EGAS00001005787
139 "SLX-15736SIGAB9HTHM2BBXXs_4"  CD8 cytotoxic                 EGAS00001005787
140 "SLX-15736SIGAB9HTHM2BBXXs_4"  Mac-cycling                   EGAS00001005787
141 "SLX-15736SIGAB9HTHM2BBXXs_4"  NK CD16pos                    EGAS00001005787
142 "SLX-15736SIGAB9HTHM2BBXXs_4"  HE                            EGAS00001005787
143 "SLX-15736SIGAB9HTHM2BBXXs_4"  Mast cell                     EGAS00001005787
144 "SLX-15736SIGAB9HTHM2BBXXs_4"  Mac-MT1                       EGAS00001005787
145 "SLX-15736SIGAB9HTHM2BBXXs_4"  DC                            EGAS00001005787
146 "SLX-15736SIGAB9HTHM2BBXXs_5"  Sperm                         EGAS00001005787
147 "SLX-15736SIGAB9HTHM2BBXXs_5"  NK CD16neg                    EGAS00001005787
148 "SLX-15736SIGAB9HTHM2BBXXs_5"  LE-KLK3                       EGAS00001005787
149 "SLX-15736SIGAB9HTHM2BBXXs_5"  LE-KLK4                       EGAS00001005787
150 "SLX-15736SIGAB9HTHM2BBXXs_5"  CE                            EGAS00001005787
151 "SLX-15736SIGAB9HTHM2BBXXs_5"  CD8 Trm                       EGAS00001005787
152 "SLX-15736SIGAB9HTHM2BBXXs_5"  CD4 naive-cm                  EGAS00001005787
153 "SLX-15736SIGAB9HTHM2BBXXs_5"  Mac1                          EGAS00001005787
154 "SLX-15736SIGAB9HTHM2BBXXs_5"  CD4 Trm                       EGAS00001005787
155 "SLX-15736SIGAB9HTHM2BBXXs_5"  HE                            EGAS00001005787
156 "SLX-15736SIGAB9HTHM2BBXXs_5"  CD8 cytotoxic                 EGAS00001005787
157 "SLX-15736SIGAB9HTHM2BBXXs_5"  Mac-cycling                   EGAS00001005787
158 "SLX-15736SIGAB9HTHM2BBXXs_5"  NK CD16pos                    EGAS00001005787
159 "SLX-15736SIGAB9HTHM2BBXXs_5"  Mast cell                     EGAS00001005787
160 "SLX-15736SIGAB9HTHM2BBXXs_5"  Mac-MT1                       EGAS00001005787
161 "SLX-15736SIGAB9HTHM2BBXXs_5"  DC                            EGAS00001005787
162 "SLX-15736SIGAD8HTHM2BBXXs_4"  LE-KLK3                       EGAS00001005787
163 "SLX-15736SIGAD8HTHM2BBXXs_4"  LE-KLK4                       EGAS00001005787
164 "SLX-15736SIGAD8HTHM2BBXXs_4"  CE                            EGAS00001005787
165 "SLX-15736SIGAD8HTHM2BBXXs_4"  B cell                        EGAS00001005787
166 "SLX-15736SIGAD8HTHM2BBXXs_4"  CD4 Trm                       EGAS00001005787
167 "SLX-15736SIGAD8HTHM2BBXXs_4"  CD8 cytotoxic                 EGAS00001005787
168 "SLX-15736SIGAD8HTHM2BBXXs_4"  CD8 Trm                       EGAS00001005787
169 "SLX-15736SIGAD8HTHM2BBXXs_4"  NK CD16neg                    EGAS00001005787
170 "SLX-15736SIGAD8HTHM2BBXXs_4"  Sperm                         EGAS00001005787
171 "SLX-15736SIGAD8HTHM2BBXXs_4"  NK CD16pos                    EGAS00001005787
172 "SLX-15736SIGAD8HTHM2BBXXs_4"  HE                            EGAS00001005787
173 "SLX-15736SIGAD8HTHM2BBXXs_4"  CD4 naive-cm                  EGAS00001005787
174 "SLX-15736SIGAD8HTHM2BBXXs_4"  BE                            EGAS00001005787
175 "SLX-15736SIGAD8HTHM2BBXXs_4"  Treg                          EGAS00001005787
176 "SLX-15736SIGAD8HTHM2BBXXs_4"  DC                            EGAS00001005787
177 "SLX-15736SIGAD8HTHM2BBXXs_4"  Mac1                          EGAS00001005787
178 "SLX-15736SIGAD8HTHM2BBXXs_4"  Endothelial                   EGAS00001005787
179 "SLX-15736SIGAD8HTHM2BBXXs_4"  Mac-MT1                       EGAS00001005787
180 "SLX-15736SIGAD8HTHM2BBXXs_4"  Mast cell                     EGAS00001005787
181 "SLX-15736SIGAD8HTHM2BBXXs_5"  LE-KLK4                       EGAS00001005787
182 "SLX-15736SIGAD8HTHM2BBXXs_5"  CE                            EGAS00001005787
183 "SLX-15736SIGAD8HTHM2BBXXs_5"  B cell                        EGAS00001005787
184 "SLX-15736SIGAD8HTHM2BBXXs_5"  CD4 Trm                       EGAS00001005787
185 "SLX-15736SIGAD8HTHM2BBXXs_5"  CD8 cytotoxic                 EGAS00001005787
186 "SLX-15736SIGAD8HTHM2BBXXs_5"  CD8 Trm                       EGAS00001005787
187 "SLX-15736SIGAD8HTHM2BBXXs_5"  LE-KLK3                       EGAS00001005787
188 "SLX-15736SIGAD8HTHM2BBXXs_5"  NK CD16neg                    EGAS00001005787
189 "SLX-15736SIGAD8HTHM2BBXXs_5"  Sperm                         EGAS00001005787
190 "SLX-15736SIGAD8HTHM2BBXXs_5"  NK CD16pos                    EGAS00001005787
191 "SLX-15736SIGAD8HTHM2BBXXs_5"  HE                            EGAS00001005787
192 "SLX-15736SIGAD8HTHM2BBXXs_5"  CD4 naive-cm                  EGAS00001005787
193 "SLX-15736SIGAD8HTHM2BBXXs_5"  BE                            EGAS00001005787
194 "SLX-15736SIGAD8HTHM2BBXXs_5"  Treg                          EGAS00001005787
195 "SLX-15736SIGAD8HTHM2BBXXs_5"  DC                            EGAS00001005787
196 "SLX-15736SIGAD8HTHM2BBXXs_5"  Mac1                          EGAS00001005787
197 "SLX-15736SIGAD8HTHM2BBXXs_5"  Endothelial                   EGAS00001005787
198 "SLX-15736SIGAD8HTHM2BBXXs_5"  Mac-MT1                       EGAS00001005787
199 "SLX-15736SIGAD8HTHM2BBXXs_5"  Mast cell                     EGAS00001005787
200 "SLX-15736SIGAE8HTHM2BBXXs_4"  LE-KLK4                       EGAS00001005787
201 "SLX-15736SIGAE8HTHM2BBXXs_4"  DC                            EGAS00001005787
202 "SLX-15736SIGAE8HTHM2BBXXs_4"  Mac-cycling                   EGAS00001005787
203 "SLX-15736SIGAE8HTHM2BBXXs_4"  LE-KLK3                       EGAS00001005787
204 "SLX-15736SIGAE8HTHM2BBXXs_4"  BE                            EGAS00001005787
205 "SLX-15736SIGAE8HTHM2BBXXs_4"  Mac1                          EGAS00001005787
206 "SLX-15736SIGAE8HTHM2BBXXs_4"  Mac-MT1                       EGAS00001005787
207 "SLX-15736SIGAE8HTHM2BBXXs_4"  CE                            EGAS00001005787
208 "SLX-15736SIGAE8HTHM2BBXXs_4"  CD8 cytotoxic                 EGAS00001005787
209 "SLX-15736SIGAE8HTHM2BBXXs_4"  NK CD16pos                    EGAS00001005787
210 "SLX-15736SIGAE8HTHM2BBXXs_4"  HE                            EGAS00001005787
211 "SLX-15736SIGAE8HTHM2BBXXs_4"  Endothelial                   EGAS00001005787
212 "SLX-15736SIGAE8HTHM2BBXXs_4"  B cell                        EGAS00001005787
213 "SLX-15736SIGAE8HTHM2BBXXs_5"  LE-KLK4                       EGAS00001005787
214 "SLX-15736SIGAE8HTHM2BBXXs_5"  DC                            EGAS00001005787
215 "SLX-15736SIGAE8HTHM2BBXXs_5"  Mac-cycling                   EGAS00001005787
216 "SLX-15736SIGAE8HTHM2BBXXs_5"  LE-KLK3                       EGAS00001005787
217 "SLX-15736SIGAE8HTHM2BBXXs_5"  Mac1                          EGAS00001005787
218 "SLX-15736SIGAE8HTHM2BBXXs_5"  BE                            EGAS00001005787
219 "SLX-15736SIGAE8HTHM2BBXXs_5"  CD8 Trm                       EGAS00001005787
220 "SLX-15736SIGAE8HTHM2BBXXs_5"  Mac-MT1                       EGAS00001005787
221 "SLX-15736SIGAE8HTHM2BBXXs_5"  CE                            EGAS00001005787
222 "SLX-15736SIGAE8HTHM2BBXXs_5"  CD4 naive-cm                  EGAS00001005787
223 "SLX-15736SIGAE8HTHM2BBXXs_5"  HE                            EGAS00001005787
224 "SLX-15736SIGAE8HTHM2BBXXs_5"  Endothelial                   EGAS00001005787
225 "SLX-15736SIGAE8HTHM2BBXXs_5"  CD8 cytotoxic                 EGAS00001005787
226 "SLX-15929SIGAC4HVLYKBBXXs_8"  LE-KLK4                       EGAS00001005787
227 "SLX-15929SIGAC4HVLYKBBXXs_8"  CD8 Trm                       EGAS00001005787
228 "SLX-15929SIGAC4HVLYKBBXXs_8"  LE-KLK3                       EGAS00001005787
229 "SLX-15929SIGAC4HVLYKBBXXs_8"  CE                            EGAS00001005787
230 "SLX-15929SIGAC4HVLYKBBXXs_8"  CD4 Trm                       EGAS00001005787
231 "SLX-15929SIGAC4HVLYKBBXXs_8"  Endothelial                   EGAS00001005787
232 "SLX-15929SIGAC4HVLYKBBXXs_8"  Fibroblast                    EGAS00001005787
233 "SLX-15929SIGAC4HVLYKBBXXs_8"  Treg                          EGAS00001005787
234 "SLX-15929SIGAC4HVLYKBBXXs_8"  BE                            EGAS00001005787
235 "SLX-15929SIGAC4HVLYKBBXXs_8"  CD4 naive-cm                  EGAS00001005787
236 "SLX-15929SIGAC4HVLYKBBXXs_8"  Sperm                         EGAS00001005787
237 "SLX-15929SIGAC4HVLYKBBXXs_8"  CD8 cytotoxic                 EGAS00001005787
238 "SLX-15929SIGAC4HVLYKBBXXs_8"  HE                            EGAS00001005787
239 "SLX-15929SIGAC4HVLYKBBXXs_8"  DC                            EGAS00001005787
240 "SLX-15929SIGAC4HVLYKBBXXs_8"  Mac1                          EGAS00001005787
241 "SLX-15929SIGAC4HVLYKBBXXs_8"  Mac2                          EGAS00001005787
242 "SLX-15929SIGAC4HVLYKBBXXs_8"  B cell                        EGAS00001005787
243 "SLX-15929SIGAC4HVLYKBBXXs_8"  NK CD16pos                    EGAS00001005787
244 "SLX-15929SIGAC4HVLYKBBXXs_8"  Mono                          EGAS00001005787
245 "SLX-15929SIGAC4HVLYKBBXXs_8"  Mast cell                     EGAS00001005787
246 "SLX-15929SIGAC4HVLYKBBXXs_8"  Mac-cycling                   EGAS00001005787
247 "SLX-15929SIGAC4HVLYKBBXXs_8"  NK CD16neg                    EGAS00001005787
248 "SLX-15929SIGAC4HVLYKBBXXs_8"  Mac-MT1                       EGAS00001005787
249 "SLX-15929SIGAD4HVLYKBBXXs_8"  Endothelial                   EGAS00001005787
250 "SLX-15929SIGAD4HVLYKBBXXs_8"  LE-KLK4                       EGAS00001005787
251 "SLX-15929SIGAD4HVLYKBBXXs_8"  CE                            EGAS00001005787
252 "SLX-15929SIGAD4HVLYKBBXXs_8"  HE                            EGAS00001005787
253 "SLX-15929SIGAD4HVLYKBBXXs_8"  DC                            EGAS00001005787
254 "SLX-15929SIGAD4HVLYKBBXXs_8"  LE-KLK3                       EGAS00001005787
255 "SLX-15929SIGAD4HVLYKBBXXs_8"  Mac2                          EGAS00001005787
256 "SLX-15929SIGAD4HVLYKBBXXs_8"  NK CD16pos                    EGAS00001005787
257 "SLX-15929SIGAD4HVLYKBBXXs_8"  B cell                        EGAS00001005787
258 "SLX-15929SIGAD4HVLYKBBXXs_8"  CD8 Trm                       EGAS00001005787
259 "SLX-15929SIGAD4HVLYKBBXXs_8"  BE                            EGAS00001005787
260 "SLX-15929SIGAD4HVLYKBBXXs_8"  CD4 naive-cm                  EGAS00001005787
261 "SLX-15929SIGAD4HVLYKBBXXs_8"  CD4 Trm                       EGAS00001005787
262 "SLX-15929SIGAG11HVLYKBBXXs_8" Endothelial                   EGAS00001005787
263 "SLX-15929SIGAG11HVLYKBBXXs_8" Sperm                         EGAS00001005787
264 "SLX-15929SIGAG11HVLYKBBXXs_8" LE-KLK4                       EGAS00001005787
265 "SLX-15929SIGAG11HVLYKBBXXs_8" LE-KLK3                       EGAS00001005787
266 "SLX-15929SIGAG11HVLYKBBXXs_8" CE                            EGAS00001005787
267 "SLX-15929SIGAG11HVLYKBBXXs_8" HE                            EGAS00001005787
268 "SLX-15929SIGAG11HVLYKBBXXs_8" Mac1                          EGAS00001005787
269 "SLX-15929SIGAG11HVLYKBBXXs_8" Mac2                          EGAS00001005787
270 "SLX-15929SIGAG11HVLYKBBXXs_8" NK cell                       EGAS00001005787
271 "SLX-15929SIGAG11HVLYKBBXXs_8" T cell                        EGAS00001005787
272 "SLX-15929SIGAG11HVLYKBBXXs_8" DC                            EGAS00001005787
273 "SLX-15929SIGAG11HVLYKBBXXs_8" BE                            EGAS00001005787
274 "SLX-15929SIGAH11HVLYKBBXXs_8" Endothelial                   EGAS00001005787
275 "SLX-15929SIGAH11HVLYKBBXXs_8" Sperm                         EGAS00001005787
276 "SLX-15929SIGAH11HVLYKBBXXs_8" LE-KLK4                       EGAS00001005787
277 "SLX-15929SIGAH11HVLYKBBXXs_8" LE-KLK3                       EGAS00001005787
278 "SLX-15929SIGAH11HVLYKBBXXs_8" CE                            EGAS00001005787
279 "SLX-15929SIGAH11HVLYKBBXXs_8" HE                            EGAS00001005787
280 "SLX-15929SIGAH11HVLYKBBXXs_8" Mac1                          EGAS00001005787
281 "SLX-15929SIGAH11HVLYKBBXXs_8" DC                            EGAS00001005787
282 "SLX-15929SIGAH11HVLYKBBXXs_8" Mac2                          EGAS00001005787
283 "SLX-15929SIGAH11HVLYKBBXXs_8" NK cell                       EGAS00001005787
284 "SLX-15929SIGAH11HVLYKBBXXs_8" BE                            EGAS00001005787
285 "SLX-15929SIGAH11HVLYKBBXXs_8" T cell                        EGAS00001005787
286 "SLX-16140SIGAB1HVMFKBBXXs_3"  CE                            EGAS00001005787
287 "SLX-16140SIGAB1HVMFKBBXXs_3"  Fibroblast                    EGAS00001005787
288 "SLX-16140SIGAB1HVMFKBBXXs_3"  LE-KLK4                       EGAS00001005787
289 "SLX-16140SIGAB1HVMFKBBXXs_3"  LE-KLK3                       EGAS00001005787
290 "SLX-16140SIGAB1HVMFKBBXXs_3"  BE                            EGAS00001005787
291 "SLX-16140SIGAB1HVMFKBBXXs_3"  NK CD16neg                    EGAS00001005787
292 "SLX-16140SIGAB1HVMFKBBXXs_3"  Sperm                         EGAS00001005787
293 "SLX-16140SIGAB1HVMFKBBXXs_3"  Endothelial                   EGAS00001005787
294 "SLX-16140SIGAB1HVMFKBBXXs_3"  Treg                          EGAS00001005787
295 "SLX-16140SIGAB1HVMFKBBXXs_3"  DC                            EGAS00001005787
296 "SLX-16140SIGAB1HVMFKBBXXs_3"  NK CD16pos                    EGAS00001005787
297 "SLX-16140SIGAB1HVMFKBBXXs_3"  HE                            EGAS00001005787
298 "SLX-16140SIGAB1HVMFKBBXXs_3"  Mast cell                     EGAS00001005787
299 "SLX-16140SIGAB1HVMFKBBXXs_3"  CD4 naive-cm                  EGAS00001005787
300 "SLX-16140SIGAB1HVMFKBBXXs_3"  CD8 cytotoxic                 EGAS00001005787
301 "SLX-16140SIGAB1HVMFKBBXXs_3"  CD8 Trm                       EGAS00001005787
302 "SLX-16140SIGAB1HVMFKBBXXs_3"  CD4 Trm                       EGAS00001005787
303 "SLX-16140SIGAB1HVMFKBBXXs_3"  Mac1                          EGAS00001005787
304 "SLX-16140SIGAC1HVMFKBBXXs_3"  LE-KLK4                       EGAS00001005787
305 "SLX-16140SIGAC1HVMFKBBXXs_3"  CE                            EGAS00001005787
306 "SLX-16140SIGAC1HVMFKBBXXs_3"  CD8 Trm                       EGAS00001005787
307 "SLX-16140SIGAC1HVMFKBBXXs_3"  Mac1                          EGAS00001005787
308 "SLX-16140SIGAC1HVMFKBBXXs_3"  BE                            EGAS00001005787
309 "SLX-16140SIGAC1HVMFKBBXXs_3"  LE-KLK3                       EGAS00001005787
310 "SLX-16140SIGAC1HVMFKBBXXs_3"  Mast cell                     EGAS00001005787
311 "SLX-16140SIGAC1HVMFKBBXXs_3"  Treg                          EGAS00001005787
312 "SLX-16140SIGAC1HVMFKBBXXs_3"  CD4 naive-cm                  EGAS00001005787
313 "SLX-16140SIGAC1HVMFKBBXXs_3"  Mac-cycling                   EGAS00001005787
314 "SLX-16140SIGAC1HVMFKBBXXs_3"  Fibroblast                    EGAS00001005787
315 "SLX-16140SIGAC1HVMFKBBXXs_3"  B cell                        EGAS00001005787
316 "SLX-16140SIGAC1HVMFKBBXXs_3"  DC                            EGAS00001005787
317 "SLX-16140SIGAC1HVMFKBBXXs_3"  Endothelial                   EGAS00001005787
318 "SLX-16140SIGAC1HVMFKBBXXs_3"  CD4 Trm                       EGAS00001005787
319 "SLX-16140SIGAC1HVMFKBBXXs_3"  Mono                          EGAS00001005787
320 "SLX-16140SIGAC1HVMFKBBXXs_3"  NK CD16pos                    EGAS00001005787
321 "SLX-16140SIGAC1HVMFKBBXXs_3"  CD8 cytotoxic                 EGAS00001005787
322 "SLX-16140SIGAC1HVMFKBBXXs_3"  Mac2                          EGAS00001005787
323 "SLX-16140SIGAC1HVMFKBBXXs_3"  NK CD16neg                    EGAS00001005787
324 "SLX-16140SIGAC1HVMFKBBXXs_3"  HE                            EGAS00001005787
325 "SLX-16140SIGAC1HVMFKBBXXs_3"  Sperm                         EGAS00001005787
326 "SLX-16140SIGAC1HVMFKBBXXs_3"  Mac-MT1                       EGAS00001005787
327 "SLX-16142SIGAG6HVMFKBBXXs_4"  HE                            EGAS00001005787
328 "SLX-16142SIGAG6HVMFKBBXXs_4"  LE-KLK3                       EGAS00001005787
329 "SLX-16142SIGAG6HVMFKBBXXs_4"  CD8 Trm                       EGAS00001005787
330 "SLX-16142SIGAG6HVMFKBBXXs_4"  BE                            EGAS00001005787
331 "SLX-16142SIGAG6HVMFKBBXXs_4"  LE-KLK4                       EGAS00001005787
332 "SLX-16142SIGAG6HVMFKBBXXs_4"  CD4 Trm                       EGAS00001005787
333 "SLX-16142SIGAG6HVMFKBBXXs_4"  Endothelial                   EGAS00001005787
334 "SLX-16142SIGAG6HVMFKBBXXs_4"  CD4 naive-cm                  EGAS00001005787
335 "SLX-16142SIGAG6HVMFKBBXXs_4"  CD8 cytotoxic                 EGAS00001005787
336 "SLX-16142SIGAG6HVMFKBBXXs_4"  CE                            EGAS00001005787
337 "SLX-16142SIGAG6HVMFKBBXXs_4"  Treg                          EGAS00001005787
338 "SLX-16142SIGAG6HVMFKBBXXs_4"  NK CD16pos                    EGAS00001005787
339 "SLX-16142SIGAG6HVMFKBBXXs_4"  Fibroblast                    EGAS00001005787
340 "SLX-16142SIGAG6HVMFKBBXXs_4"  NK CD16neg                    EGAS00001005787
341 "SLX-16142SIGAG6HVMFKBBXXs_4"  DC                            EGAS00001005787
342 "SLX-16142SIGAG6HVMFKBBXXs_4"  Sperm                         EGAS00001005787
343 "SLX-16142SIGAG6HVMFKBBXXs_4"  Mac1                          EGAS00001005787
344 "SLX-16142SIGAG6HVMFKBBXXs_4"  B cell                        EGAS00001005787
345 "SLX-16142SIGAG6HVMFKBBXXs_4"  Mono                          EGAS00001005787
346 "SLX-16142SIGAG6HVMFKBBXXs_4"  Mast cell                     EGAS00001005787
347 "SLX-16142SIGAG6HVMFKBBXXs_4"  Mac-cycling                   EGAS00001005787
348 "SLX-16142SIGAG6HVMFKBBXXs_4"  Mac2                          EGAS00001005787
349 "SLX-16142SIGAH6HVMFKBBXXs_4"  LE-KLK4                       EGAS00001005787
350 "SLX-16142SIGAH6HVMFKBBXXs_4"  LE-KLK3                       EGAS00001005787
351 "SLX-16142SIGAH6HVMFKBBXXs_4"  CE                            EGAS00001005787
352 "SLX-16142SIGAH6HVMFKBBXXs_4"  Treg                          EGAS00001005787
353 "SLX-16142SIGAH6HVMFKBBXXs_4"  CD4 Trm                       EGAS00001005787
354 "SLX-16142SIGAH6HVMFKBBXXs_4"  CD8 cytotoxic                 EGAS00001005787
355 "SLX-16142SIGAH6HVMFKBBXXs_4"  B cell                        EGAS00001005787
356 "SLX-16142SIGAH6HVMFKBBXXs_4"  NK CD16neg                    EGAS00001005787
357 "SLX-16142SIGAH6HVMFKBBXXs_4"  Endothelial                   EGAS00001005787
358 "SLX-16142SIGAH6HVMFKBBXXs_4"  CD8 Trm                       EGAS00001005787
359 "SLX-16142SIGAH6HVMFKBBXXs_4"  BE                            EGAS00001005787
360 "SLX-16142SIGAH6HVMFKBBXXs_4"  HE                            EGAS00001005787
361 "SLX-16142SIGAH6HVMFKBBXXs_4"  DC                            EGAS00001005787
362 "SLX-16142SIGAH6HVMFKBBXXs_4"  Mac1                          EGAS00001005787
363 "SLX-16142SIGAH6HVMFKBBXXs_4"  CD4 naive-cm                  EGAS00001005787
364 "SLX-16142SIGAH6HVMFKBBXXs_4"  Sperm                         EGAS00001005787
365 "SLX-16142SIGAH6HVMFKBBXXs_4"  Fibroblast                    EGAS00001005787
366 "SLX-16142SIGAH6HVMFKBBXXs_4"  NK CD16pos                    EGAS00001005787
367 "SLX-16142SIGAH6HVMFKBBXXs_4"  Mono                          EGAS00001005787
368 "SLX-16142SIGAH6HVMFKBBXXs_4"  Mast cell                     EGAS00001005787
369 "SLX-16147SIGAE7HVMFKBBXXs_7"  CD4 naive-cm                  EGAS00001005787
370 "SLX-16147SIGAE7HVMFKBBXXs_7"  LE-KLK4                       EGAS00001005787
371 "SLX-16147SIGAE7HVMFKBBXXs_7"  B cell                        EGAS00001005787
372 "SLX-16147SIGAE7HVMFKBBXXs_7"  Endothelial                   EGAS00001005787
373 "SLX-16147SIGAE7HVMFKBBXXs_7"  LE-KLK3                       EGAS00001005787
374 "SLX-16147SIGAE7HVMFKBBXXs_7"  CE                            EGAS00001005787
375 "SLX-16147SIGAE7HVMFKBBXXs_7"  CD4 Trm                       EGAS00001005787
376 "SLX-16147SIGAE7HVMFKBBXXs_7"  Fibroblast                    EGAS00001005787
377 "SLX-16147SIGAE7HVMFKBBXXs_7"  CD8 Trm                       EGAS00001005787
378 "SLX-16147SIGAE7HVMFKBBXXs_7"  BE                            EGAS00001005787
379 "SLX-16147SIGAE7HVMFKBBXXs_7"  HE                            EGAS00001005787
380 "SLX-16147SIGAE7HVMFKBBXXs_7"  CD8 cytotoxic                 EGAS00001005787
381 "SLX-16147SIGAE7HVMFKBBXXs_7"  Mast cell                     EGAS00001005787
382 "SLX-16147SIGAE7HVMFKBBXXs_7"  Sperm                         EGAS00001005787
383 "SLX-16147SIGAE7HVMFKBBXXs_7"  NK CD16neg                    EGAS00001005787
384 "SLX-16147SIGAE7HVMFKBBXXs_7"  NK CD16pos                    EGAS00001005787
385 "SLX-16147SIGAE7HVMFKBBXXs_7"  DC                            EGAS00001005787
386 "SLX-16147SIGAE7HVMFKBBXXs_7"  Treg                          EGAS00001005787
387 "SLX-16147SIGAF7HVMFKBBXXs_7"  LE-KLK4                       EGAS00001005787
388 "SLX-16147SIGAF7HVMFKBBXXs_7"  CE                            EGAS00001005787
389 "SLX-16147SIGAF7HVMFKBBXXs_7"  CD8 Trm                       EGAS00001005787
390 "SLX-16147SIGAF7HVMFKBBXXs_7"  LE-KLK3                       EGAS00001005787
391 "SLX-16147SIGAF7HVMFKBBXXs_7"  BE                            EGAS00001005787
392 "SLX-16147SIGAF7HVMFKBBXXs_7"  Endothelial                   EGAS00001005787
393 "SLX-16147SIGAF7HVMFKBBXXs_7"  CD4 naive-cm                  EGAS00001005787
394 "SLX-16147SIGAF7HVMFKBBXXs_7"  HE                            EGAS00001005787
395 "SLX-16147SIGAF7HVMFKBBXXs_7"  Fibroblast                    EGAS00001005787
396 "SLX-16147SIGAF7HVMFKBBXXs_7"  CD4 Trm                       EGAS00001005787
397 "SLX-16147SIGAF7HVMFKBBXXs_7"  DC                            EGAS00001005787
398 "SLX-16147SIGAF7HVMFKBBXXs_7"  Mast cell                     EGAS00001005787
399 "SLX-16147SIGAF7HVMFKBBXXs_7"  CD8 cytotoxic                 EGAS00001005787
400 "SLX-16148SIGAG7HVMFKBBXXs_8"  LE-KLK4                       EGAS00001005787
401 "SLX-16148SIGAG7HVMFKBBXXs_8"  Endothelial                   EGAS00001005787
402 "SLX-16148SIGAG7HVMFKBBXXs_8"  LE-KLK3                       EGAS00001005787
403 "SLX-16148SIGAG7HVMFKBBXXs_8"  HE                            EGAS00001005787
404 "SLX-16148SIGAG7HVMFKBBXXs_8"  CE                            EGAS00001005787
405 "SLX-16148SIGAG7HVMFKBBXXs_8"  BE                            EGAS00001005787
406 "SLX-16148SIGAG7HVMFKBBXXs_8"  T cell                        EGAS00001005787
407 "SLX-16148SIGAG7HVMFKBBXXs_8"  Mac1                          EGAS00001005787
408 "SLX-16148SIGAG7HVMFKBBXXs_8"  DC                            EGAS00001005787
409 "SLX-16148SIGAG7HVMFKBBXXs_8"  Mac2                          EGAS00001005787
410 "SLX-16148SIGAG7HVMFKBBXXs_8"  Sperm                         EGAS00001005787
411 "SLX-16148SIGAG7HVMFKBBXXs_8"  Fibroblast                    EGAS00001005787
412 "SLX-16148SIGAH7HVMFKBBXXs_8"  LE-KLK4                       EGAS00001005787
413 "SLX-16148SIGAH7HVMFKBBXXs_8"  LE-KLK3                       EGAS00001005787
414 "SLX-16148SIGAH7HVMFKBBXXs_8"  CE                            EGAS00001005787
415 "SLX-16148SIGAH7HVMFKBBXXs_8"  BE                            EGAS00001005787
416 "SLX-16148SIGAH7HVMFKBBXXs_8"  T cell                        EGAS00001005787
417 "SLX-16148SIGAH7HVMFKBBXXs_8"  Mac2                          EGAS00001005787
418 "SLX-16148SIGAH7HVMFKBBXXs_8"  Mac1                          EGAS00001005787
419 "SLX-16148SIGAH7HVMFKBBXXs_8"  Sperm                         EGAS00001005787
420 "SLX-16148SIGAH7HVMFKBBXXs_8"  Fibroblast                    EGAS00001005787
421 "SLX-16362SIGAA3HWFTVBBXXs_4"  LE-KLK3                       EGAS00001005787
422 "SLX-16362SIGAA3HWFTVBBXXs_4"  CD8 Trm                       EGAS00001005787
423 "SLX-16362SIGAA3HWFTVBBXXs_4"  LE-KLK4                       EGAS00001005787
424 "SLX-16362SIGAA3HWFTVBBXXs_4"  Fibroblast                    EGAS00001005787
425 "SLX-16362SIGAA3HWFTVBBXXs_4"  CD4 naive-cm                  EGAS00001005787
426 "SLX-16362SIGAA3HWFTVBBXXs_4"  Endothelial                   EGAS00001005787
427 "SLX-16362SIGAA3HWFTVBBXXs_4"  BE                            EGAS00001005787
428 "SLX-16362SIGAA3HWFTVBBXXs_4"  NK CD16neg                    EGAS00001005787
429 "SLX-16362SIGAA3HWFTVBBXXs_4"  Treg                          EGAS00001005787
430 "SLX-16362SIGAA3HWFTVBBXXs_4"  CE                            EGAS00001005787
431 "SLX-16362SIGAA3HWFTVBBXXs_4"  HE                            EGAS00001005787
432 "SLX-16362SIGAA3HWFTVBBXXs_4"  CD8 cytotoxic                 EGAS00001005787
433 "SLX-16362SIGAA3HWFTVBBXXs_4"  Mast cell                     EGAS00001005787
434 "SLX-16362SIGAA3HWFTVBBXXs_4"  CD4 Trm                       EGAS00001005787
435 "SLX-16362SIGAA3HWFTVBBXXs_4"  NK CD16pos                    EGAS00001005787
436 "SLX-16362SIGAA3HWFTVBBXXs_4"  B cell                        EGAS00001005787
437 "SLX-16362SIGAA3HWFTVBBXXs_4"  Sperm                         EGAS00001005787
438 "SLX-16362SIGAA3HWFTVBBXXs_4"  Mac-cycling                   EGAS00001005787
439 "SLX-16362SIGAA3HWFTVBBXXs_4"  Mac1                          EGAS00001005787
440 "SLX-16362SIGAA3HWFTVBBXXs_4"  DC                            EGAS00001005787
441 "SLX-16362SIGAB3HWFTVBBXXs_4"  LE-KLK4                       EGAS00001005787
442 "SLX-16362SIGAB3HWFTVBBXXs_4"  LE-KLK3                       EGAS00001005787
443 "SLX-16362SIGAB3HWFTVBBXXs_4"  CE                            EGAS00001005787
444 "SLX-16362SIGAB3HWFTVBBXXs_4"  BE                            EGAS00001005787
445 "SLX-16362SIGAB3HWFTVBBXXs_4"  DC                            EGAS00001005787
446 "SLX-16362SIGAB3HWFTVBBXXs_4"  Fibroblast                    EGAS00001005787
447 "SLX-16362SIGAB3HWFTVBBXXs_4"  Endothelial                   EGAS00001005787
448 "SLX-16362SIGAB3HWFTVBBXXs_4"  HE                            EGAS00001005787
449 "SLX-16362SIGAB3HWFTVBBXXs_4"  CD8 Trm                       EGAS00001005787
450 "SLX-16362SIGAB3HWFTVBBXXs_4"  Mac1                          EGAS00001005787
451 "GSM4089151"                   Epithelial cell               GSE137829      
452 "GSM4089151"                   Myeloid                       GSE137829      
453 "GSM4089151"                   T cell                        GSE137829      
454 "GSM4089151"                   B cell                        GSE137829      
455 "GSM4089151"                   Myofibroblast                 GSE137829      
456 "GSM4089151"                   Endothelial cell              GSE137829      
457 "GSM4089151"                   Fibroblast                    GSE137829      
458 "GSM4089152"                   Epithelial cell               GSE137829      
459 "GSM4089152"                   Myeloid                       GSE137829      
460 "GSM4089152"                   B cell                        GSE137829      
461 "GSM4089152"                   T cell                        GSE137829      
462 "GSM4089152"                   Fibroblast                    GSE137829      
463 "GSM4089152"                   Endothelial cell              GSE137829      
464 "GSM4089153"                   Fibroblast                    GSE137829      
465 "GSM4089153"                   Epithelial cell               GSE137829      
466 "GSM4089153"                   Myeloid                       GSE137829      
467 "GSM4089153"                   Endothelial cell              GSE137829      
468 "GSM4089153"                   T cell                        GSE137829      
469 "GSM4089153"                   Myofibroblast                 GSE137829      
470 "GSM4089153"                   B cell                        GSE137829      
471 "GSM4089154"                   Epithelial cell               GSE137829      
472 "GSM4089154"                   Endothelial cell              GSE137829      
473 "GSM4089154"                   T cell                        GSE137829      
474 "GSM4089154"                   Myofibroblast                 GSE137829      
475 "GSM4089154"                   Myeloid                       GSE137829      
476 "GSM4089154"                   B cell                        GSE137829      
477 "GSM4089154"                   Fibroblast                    GSE137829      
478 "GSM4711414"                   Fibroblast                    GSE137829      
479 "GSM4711414"                   T cell                        GSE137829      
480 "GSM4711414"                   Myofibroblast                 GSE137829      
481 "GSM4711414"                   Epithelial cell               GSE137829      
482 "GSM4711414"                   B cell                        GSE137829      
483 "GSM4711414"                   Endothelial cell              GSE137829      
484 "GSM4711414"                   mast cell                     GSE137829      
485 "GSM4711414"                   Myeloid                       GSE137829      
486 "GSM4711415"                   Fibroblast                    GSE137829      
487 "GSM4711415"                   Epithelial cell               GSE137829      
488 "GSM4711415"                   T cell                        GSE137829      
489 "GSM4711415"                   Endothelial cell              GSE137829      
490 "GSM4711415"                   Myofibroblast                 GSE137829      
491 "GSM4711415"                   Myeloid                       GSE137829      
492 "GSM4711415"                   mast cell                     GSE137829      
493 "GSM4711415"                   B cell                        GSE137829      
494 "GSM4203181"                   Luminal                       GSE141445      
495 "GSM4203181"                   T                             GSE141445      
496 "GSM4203181"                   Fibroblast                    GSE141445      
497 "GSM4203181"                   Basal/intermediate            GSE141445      
498 "GSM4203181"                   Mast                          GSE141445      
499 "GSM4203181"                   Monocytic                     GSE141445      
500 "GSM4203181"                   Endothelial                   GSE141445      
501 "AUG_PB1"                      Epithelial_cells              GSE176031      
502 "AUG_PB1"                      Endothelial_cells             GSE176031      
503 "AUG_PB1"                      Smooth_muscle_cells           GSE176031      
504 "AUG_PB1"                      Monocyte                      GSE176031      
505 "AUG_PB1"                      Monocytes                     GSE176031      
506 "AUG_PB1"                      Plasma cells                  GSE176031      
507 "AUG_PB1"                      Apidocytes                    GSE176031      
508 "AUG_PB1"                      CD8+ Tem                      GSE176031      
509 "AUG_PB1"                      Pre-B_cell_CD34-              GSE176031      
510 "PR5249_N"                     Epithelial_cells              GSE176031      
511 "PR5249_N"                     Endothelial_cells             GSE176031      
512 "PR5249_N"                     Monocyte                      GSE176031      
513 "PR5249_N"                     Apidocytes                    GSE176031      
514 "PR5249_N"                     Macrophage                    GSE176031      
515 "PR5249_N"                     Monocytes                     GSE176031      
516 "PR5249_N"                     Smooth_muscle_cells           GSE176031      
517 "PR5249_N"                     Plasma cells                  GSE176031      
518 "PR5249_N"                     CD8+ Tem                      GSE176031      
519 "PR5249_N"                     Pre-B_cell_CD34-              GSE176031      
520 "PR5249_T"                     Epithelial_cells              GSE176031      
521 "PR5249_T"                     Macrophage                    GSE176031      
522 "PR5249_T"                     CD8+ Tem                      GSE176031      
523 "PR5249_T"                     Monocyte                      GSE176031      
524 "PR5249_T"                     Endothelial_cells             GSE176031      
525 "PR5249_T"                     Monocytes                     GSE176031      
526 "PR5249_T"                     Smooth_muscle_cells           GSE176031      
527 "PR5249_T"                     Apidocytes                    GSE176031      
528 "PR5251_N"                     Epithelial_cells              GSE176031      
529 "PR5251_N"                     Monocytes                     GSE176031      
530 "PR5251_N"                     Endothelial_cells             GSE176031      
531 "PR5251_N"                     Monocyte                      GSE176031      
532 "PR5251_N"                     Macrophage                    GSE176031      
533 "PR5251_N"                     CD8+ Tem                      GSE176031      
534 "PR5251_N"                     Smooth_muscle_cells           GSE176031      
535 "PR5251_N"                     NK_cell                       GSE176031      
536 "PR5251_N"                     Apidocytes                    GSE176031      
537 "PR5251_N"                     Pre-B_cell_CD34-              GSE176031      
538 "PR5251_N"                     Plasma cells                  GSE176031      
539 "PR5251_T"                     Epithelial_cells              GSE176031      
540 "PR5251_T"                     Macrophage                    GSE176031      
541 "PR5251_T"                     Monocytes                     GSE176031      
542 "PR5251_T"                     Monocyte                      GSE176031      
543 "PR5251_T"                     Apidocytes                    GSE176031      
544 "PR5251_T"                     CD8+ Tem                      GSE176031      
545 "PR5251_T"                     Pre-B_cell_CD34-              GSE176031      
546 "PR5251_T"                     Endothelial_cells             GSE176031      
547 "PR5251_T"                     NK_cell                       GSE176031      
548 "PR5251_T"                     Smooth_muscle_cells           GSE176031      
549 "PR5251_T"                     Plasma cells                  GSE176031      
550 "PR5254_N"                     Epithelial_cells              GSE176031      
551 "PR5254_N"                     Macrophage                    GSE176031      
552 "PR5254_N"                     Apidocytes                    GSE176031      
553 "PR5254_N"                     Endothelial_cells             GSE176031      
554 "PR5254_N"                     Monocyte                      GSE176031      
555 "PR5254_N"                     Smooth_muscle_cells           GSE176031      
556 "PR5254_N"                     NK_cell                       GSE176031      
557 "PR5254_N"                     CD8+ Tem                      GSE176031      
558 "PR5254_N"                     Plasma cells                  GSE176031      
559 "PR5254_N"                     Monocytes                     GSE176031      
560 "PR5254_T"                     Epithelial_cells              GSE176031      
561 "PR5254_T"                     Endothelial_cells             GSE176031      
562 "PR5254_T"                     CD8+ Tem                      GSE176031      
563 "PR5254_T"                     Apidocytes                    GSE176031      
564 "PR5254_T"                     Smooth_muscle_cells           GSE176031      
565 "PR5254_T"                     Monocytes                     GSE176031      
566 "PR5254_T"                     Monocyte                      GSE176031      
567 "PR5254_T"                     NK_cell                       GSE176031      
568 "PR5254_T"                     Macrophage                    GSE176031      
569 "PR5254_T"                     Plasma cells                  GSE176031      
570 "PR5261_N"                     Epithelial_cells              GSE176031      
571 "PR5261_N"                     Endothelial_cells             GSE176031      
572 "PR5261_N"                     Apidocytes                    GSE176031      
573 "PR5261_N"                     Monocyte                      GSE176031      
574 "PR5261_N"                     Smooth_muscle_cells           GSE176031      
575 "PR5261_N"                     Monocytes                     GSE176031      
576 "PR5261_N"                     CD8+ Tem                      GSE176031      
577 "PR5261_N"                     Macrophage                    GSE176031      
578 "PR5261_N"                     NK_cell                       GSE176031      
579 "PR5261_T"                     Epithelial_cells              GSE176031      
580 "PR5261_T"                     Endothelial_cells             GSE176031      
581 "PR5261_T"                     Apidocytes                    GSE176031      
582 "PR5261_T"                     Smooth_muscle_cells           GSE176031      
583 "PR5261_T"                     Monocyte                      GSE176031      
584 "PR5261_T"                     Monocytes                     GSE176031      
585 "PR5261_T"                     NK_cell                       GSE176031      
586 "PR5261_T"                     Plasma cells                  GSE176031      
587 "PR5261_T"                     CD8+ Tem                      GSE176031      
588 "PR5269"                       Epithelial_cells              GSE176031      
589 "PR5269"                       Monocytes                     GSE176031      
590 "PR5269"                       Monocyte                      GSE176031      
591 "PR5269"                       Endothelial_cells             GSE176031      
592 "PR5269"                       Macrophage                    GSE176031      
593 "PR5269"                       Apidocytes                    GSE176031      
594 "PR5269"                       CD8+ Tem                      GSE176031      
595 "PR5269"                       Smooth_muscle_cells           GSE176031      
596 "PR5269"                       Pre-B_cell_CD34-              GSE176031      
597 "PR5269"                       Plasma cells                  GSE176031      
598 "PR5269"                       NK_cell                       GSE176031      
599 "MAY_PB1"                      Epithelial_cells              GSE176031      
600 "MAY_PB1"                      Monocytes                     GSE176031      
601 "MAY_PB1"                      Endothelial_cells             GSE176031      
602 "MAY_PB1"                      Apidocytes                    GSE176031      
603 "MAY_PB1"                      Smooth_muscle_cells           GSE176031      
604 "MAY_PB1"                      Monocyte                      GSE176031      
605 "MAY_PB1"                      Plasma cells                  GSE176031      
606 "MAY_PB1"                      Macrophage                    GSE176031      
607 "MAY_PB1"                      CD8+ Tem                      GSE176031      
608 "MAY_PB1"                      NK_cell                       GSE176031      
609 "MAY_PB1"                      Pre-B_cell_CD34-              GSE176031      
610 "MAY_PB2"                      Endothelial_cells             GSE176031      
611 "MAY_PB2"                      Epithelial_cells              GSE176031      
612 "MAY_PB2"                      Monocyte                      GSE176031      
613 "MAY_PB2"                      Macrophage                    GSE176031      
614 "MAY_PB2"                      Apidocytes                    GSE176031      
615 "MAY_PB2"                      Smooth_muscle_cells           GSE176031      
616 "MAY_PB2"                      CD8+ Tem                      GSE176031      
617 "MAY_PB2"                      Monocytes                     GSE176031      
618 "MAY_PB2"                      Plasma cells                  GSE176031      
619 "MAY_PB2"                      Pre-B_cell_CD34-              GSE176031      
620 "MAY_PB2"                      NK_cell                       GSE176031      
621 "PR5186"                       Macrophage                    GSE176031      
622 "PR5186"                       Epithelial_cells              GSE176031      
623 "PR5186"                       Apidocytes                    GSE176031      
624 "PR5186"                       Monocyte                      GSE176031      
625 "PR5186"                       Monocytes                     GSE176031      
626 "PR5186"                       Plasma cells                  GSE176031      
627 "PR5186"                       Endothelial_cells             GSE176031      
628 "PR5186"                       NK_cell                       GSE176031      
629 "PR5186"                       CD8+ Tem                      GSE176031      
630 "PR5186"                       Smooth_muscle_cells           GSE176031      
631 "PR5186"                       Pre-B_cell_CD34-              GSE176031      
632 "PR5196"                       Epithelial_cells              GSE176031      
633 "PR5196"                       Macrophage                    GSE176031      
634 "PR5196"                       Monocytes                     GSE176031      
635 "PR5196"                       Monocyte                      GSE176031      
636 "PR5196"                       CD8+ Tem                      GSE176031      
637 "PR5196"                       Endothelial_cells             GSE176031      
638 "PR5196"                       Plasma cells                  GSE176031      
639 "PR5196"                       Pre-B_cell_CD34-              GSE176031      
640 "PR5196"                       Smooth_muscle_cells           GSE176031      
641 "PR5196"                       Apidocytes                    GSE176031      
642 "PR5196"                       NK_cell                       GSE176031      
643 "PR5199"                       Epithelial_cells              GSE176031      
644 "PR5199"                       Macrophage                    GSE176031      
645 "PR5199"                       Monocytes                     GSE176031      
646 "PR5199"                       Monocyte                      GSE176031      
647 "PR5199"                       Apidocytes                    GSE176031      
648 "PR5199"                       Endothelial_cells             GSE176031      
649 "PR5199"                       Smooth_muscle_cells           GSE176031      
650 "PR5199"                       NK_cell                       GSE176031      
651 "PR5199"                       CD8+ Tem                      GSE176031      
652 "PR5199"                       Pre-B_cell_CD34-              GSE176031

stemangiola commented 2 years ago

Thanks Xinpu.

please encase the code or results in

quotation, like I do here (you can see the markdown if you click on edit on my comment)


#R Code here
library(tidyseurat)
library(purrr)
library(job)

#parsed seurat data
dir="dev/xinpu_datascript/parsed_data/"
files<-list.files(path=dir,pattern='_final.rds')
folder<-paste0(dir,files)
assay_list<-lapply(folder,readRDS)
prostate_samples<-assay_list%>%purrr::reduce(tidyseurat::bind_rows)
#put into background
job::job({saveRDS(prostate_samples,file='dev/xinpu_datascript/parsed_data/5datasets.rds')})

#get cell number per sample
prostate_samples%>%count(dataset,sample)%>% print(n = Inf)


# Results here
# Get cell number per dataset per sample
# A tibble: 51 × 3
   dataset         sample                             n
   <chr>           <chr>                          <int>
 1 EGAS00001005115 " M-P1"                        10224
 2 EGAS00001005115 "BC-P1"                        11115
 3 EGAS00001005115 "BC-P2"                        11763
 4 EGAS00001005115 "BC-P3"                         7154
 5 EGAS00001005115 "PC-P1"                         8723
 6 EGAS00001005787 "SLX-15732SIGAC4HTVNWBBXXs_6"   1887
 7 EGAS00001005787 "SLX-15732SIGAD4HTVNWBBXXs_6"   2687
 8 EGAS00001005787 "SLX-15736SIGAA9HTHM2BBXXs_4"    838
 9 EGAS00001005787 "SLX-15736SIGAA9HTHM2BBXXs_5"    841
10 EGAS00001005787 "SLX-15736SIGAB9HTHM2BBXXs_4"   1064
11 EGAS00001005787 "SLX-15736SIGAB9HTHM2BBXXs_5"   1056
12 EGAS00001005787 "SLX-15736SIGAD8HTHM2BBXXs_4"    857
13 EGAS00001005787 "SLX-15736SIGAD8HTHM2BBXXs_5"    844
14 EGAS00001005787 "SLX-15736SIGAE8HTHM2BBXXs_4"    250
15 EGAS00001005787 "SLX-15736SIGAE8HTHM2BBXXs_5"    244
16 EGAS00001005787 "SLX-15929SIGAC4HVLYKBBXXs_8"   1099
17 EGAS00001005787 "SLX-15929SIGAD4HVLYKBBXXs_8"    111
18 EGAS00001005787 "SLX-15929SIGAG11HVLYKBBXXs_8"    88
19 EGAS00001005787 "SLX-15929SIGAH11HVLYKBBXXs_8"   103
20 EGAS00001005787 "SLX-16140SIGAB1HVMFKBBXXs_3"    148
21 EGAS00001005787 "SLX-16140SIGAC1HVMFKBBXXs_3"    858
22 EGAS00001005787 "SLX-16142SIGAG6HVMFKBBXXs_4"    699
23 EGAS00001005787 "SLX-16142SIGAH6HVMFKBBXXs_4"   1136
24 EGAS00001005787 "SLX-16147SIGAE7HVMFKBBXXs_7"    486
25 EGAS00001005787 "SLX-16147SIGAF7HVMFKBBXXs_7"    613
26 EGAS00001005787 "SLX-16148SIGAG7HVMFKBBXXs_8"    221
27 EGAS00001005787 "SLX-16148SIGAH7HVMFKBBXXs_8"     91
28 EGAS00001005787 "SLX-16362SIGAA3HWFTVBBXXs_4"    692
29 EGAS00001005787 "SLX-16362SIGAB3HWFTVBBXXs_4"    195
30 GSE137829       "GSM4089151"                    3022
31 GSE137829       "GSM4089152"                     950
32 GSE137829       "GSM4089153"                     965
33 GSE137829       "GSM4089154"                    1062
34 GSE137829       "GSM4711414"                    8690
35 GSE137829       "GSM4711415"                    6603
36 GSE141445       "GSM4203181"                   36424
37 GSE176031       "AUG_PB1"                        933
38 GSE176031       "MAY_PB1"                       3568
39 GSE176031       "MAY_PB2"                       2135
40 GSE176031       "PR5186"                         763
41 GSE176031       "PR5196"                        1993
42 GSE176031       "PR5199"                        1025
43 GSE176031       "PR5249_N"                      1683
44 GSE176031       "PR5249_T"                       810
45 GSE176031       "PR5251_N"                      1135
46 GSE176031       "PR5251_T"                      1830
47 GSE176031       "PR5254_N"                       980
48 GSE176031       "PR5254_T"                       493
49 GSE176031       "PR5261_N"                       934
50 GSE176031       "PR5261_T"                      1561
51 GSE176031       "PR5269"                        1900

# Get cell type per sample
prostate_samples%>%distinct(dataset,sample,cell_type)%>% print(n = Inf)

We need to get cell type per dataset.

# A tibble: 73 × 2
   cell_type                     dataset        
   <chr>                         <chr>          
 1 Endothelial                   EGAS00001005115
 2 Cancer/Epithelial             EGAS00001005115
 3 Monocytes/Macrophages         EGAS00001005115
 4 PVL cells                     EGAS00001005115
 5 CAFs                          EGAS00001005115
 6 Cancer/Epithelial Cycling     EGAS00001005115
 7 T-cells                       EGAS00001005115
 8 Plasmablasts                  EGAS00001005115
 9 B-cells                       EGAS00001005115
10 Myoepithelial                 EGAS00001005115
11 Doublets                      EGAS00001005115
12 T-cells Cycling               EGAS00001005115
13 Mouse 3T3 spike-in            EGAS00001005115
14 Unassigned                    EGAS00001005115
15 pDCs                          EGAS00001005115
16 Monocytes/Macrophages Cycling EGAS00001005115
17 cDCs                          EGAS00001005115
18 NK cells                      EGAS00001005115
19 MAST cells                    EGAS00001005115
20 Cancer                        EGAS00001005115
21 Endothelial 1                 EGAS00001005115
22 Endothelial 2                 EGAS00001005115
23 T cell                        EGAS00001005787
24 Mac1                          EGAS00001005787
25 Endothelial                   EGAS00001005787
26 LE-KLK3                       EGAS00001005787
27 DC                            EGAS00001005787
28 NK cell                       EGAS00001005787
29 Mono                          EGAS00001005787
30 Mast cell                     EGAS00001005787
31 CE                            EGAS00001005787
32 Mac-MT1                       EGAS00001005787
33 LE-KLK4                       EGAS00001005787
34 Sperm                         EGAS00001005787
35 BE                            EGAS00001005787
36 Mac2                          EGAS00001005787
37 HE                            EGAS00001005787
38 Fibroblast                    EGAS00001005787
39 B cell                        EGAS00001005787
40 CD4 naive-cm                  EGAS00001005787
41 CD8 cytotoxic                 EGAS00001005787
42 CD4 Trm                       EGAS00001005787
43 NK CD16pos                    EGAS00001005787
44 Treg                          EGAS00001005787
45 CD8 Trm                       EGAS00001005787
46 NK CD16neg                    EGAS00001005787
47 Mac-cycling                   EGAS00001005787
48 Epithelial cell               GSE137829      
49 Myeloid                       GSE137829      
50 T cell                        GSE137829      
51 B cell                        GSE137829      
52 Myofibroblast                 GSE137829      
53 Endothelial cell              GSE137829      
54 Fibroblast                    GSE137829      
55 mast cell                     GSE137829      
56 Luminal                       GSE141445      
57 T                             GSE141445      
58 Fibroblast                    GSE141445      
59 Basal/intermediate            GSE141445      
60 Mast                          GSE141445      
61 Monocytic                     GSE141445      
62 Endothelial                   GSE141445      
63 Epithelial_cells              GSE176031      
64 Endothelial_cells             GSE176031      
65 Smooth_muscle_cells           GSE176031      
66 Monocyte                      GSE176031      
67 Monocytes                     GSE176031      
68 Plasma cells                  GSE176031      
69 Apidocytes                    GSE176031      
70 CD8+ Tem                      GSE176031      
71 Pre-B_cell_CD34-              GSE176031      
72 Macrophage                    GSE176031      
73 NK_cell                       GSE176031

stemangiola commented 2 years ago

quotation, like I do here (you can see the markdown if you click on edit on my comment)

stemangiola / cellsig

First explorative tasks #60