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1 Data Summary


2 BridgeSettings

Configuration Settings for the Workflow

species tissue metadata genesets genetype min_umi_per_cell max_mt_percent min_genes_per_cell min_cell scr_th seu_nrmlz_method seu_scale_factor seu_n_hvg seu_n_dim seu_k_param seu_cluster_res harmony tsne spr_n_dim mrk_logfc mrk_min_pct mrk_only_pos mrk_test mrk_top_n adt trajectory traj_var_gene traj_top_n pipe_version
hs skin sample_based none none 750 10 250 3 0 LogNormalize 1e+06 2000 30 20 0.7 sample FALSE 30 0.25 0.5 TRUE wilcox 25 FALSE none 1000 50 1.0.0

3 BridgeQC

3.1 Sample-level Characteristics and Quality Control Metrics

3.1.1 Metadata

sample stage tissue site age disease enrichment location sex sample_id
4820STDY7388991 adult Dermis non_lesion Unknown Healthy Fibroblasts Breast Female S1
4820STDY7388992 adult Dermis non_lesion Unknown Healthy Lymphocytes Breast Female S2
4820STDY7388993 adult Dermis non_lesion Unknown Healthy Endothelium Breast Female S3
4820STDY7388994 adult Dermis non_lesion Unknown Healthy APCs Breast Female S4
4820STDY7388995 adult Epidermis non_lesion Unknown Healthy APCs Breast Female S5
4820STDY7388996 adult Epidermis non_lesion Unknown Healthy CD49fN_KC Breast Female S6
4820STDY7388997 adult Epidermis non_lesion Unknown Healthy CD49fP_KC Breast Female S7
4820STDY7388998 adult Epidermis non_lesion Unknown Healthy Lymphocytes Breast Female S8
4820STDY7388999 adult Dermis non_lesion Unknown Healthy Fibroblasts Breast Female S9
4820STDY7389000 adult Dermis non_lesion Unknown Healthy Lymphocytes Breast Female S10
4820STDY7389001 adult Dermis non_lesion Unknown Healthy Endothelium Breast Female S11
4820STDY7389002 adult Dermis non_lesion Unknown Healthy APCs Breast Female S12
4820STDY7389003 adult Epidermis non_lesion Unknown Healthy APCs Breast Female S13
4820STDY7389004 adult Epidermis non_lesion Unknown Healthy CD49fN_KC Breast Female S14
4820STDY7389005 adult Epidermis non_lesion Unknown Healthy CD49fP_KC Breast Female S15
4820STDY7389006 adult Epidermis non_lesion Unknown Healthy Lymphocytes Breast Female S16
4820STDY7389007 adult Dermis non_lesion Unknown Healthy Fibroblasts Breast Female S17
4820STDY7389008 adult Dermis non_lesion Unknown Healthy Lymphocytes Breast Female S18
4820STDY7389009 adult Dermis non_lesion Unknown Healthy Endothelium Breast Female S19
4820STDY7389010 adult Dermis non_lesion Unknown Healthy APCs Breast Female S20
4820STDY7389011 adult Epidermis non_lesion Unknown Healthy APCs Breast Female S21
4820STDY7389012 adult Epidermis non_lesion Unknown Healthy CD49fN_KC Breast Female S22
4820STDY7389013 adult Epidermis non_lesion Unknown Healthy CD49fP_KC Breast Female S23
4820STDY7389014 adult Epidermis non_lesion Unknown Healthy Lymphocytes Breast Female S24
SKN8090524 adult Epidermis non_lesion 62 Eczema Live_single_spike Lower_back Female S25
SKN8090525 adult Epidermis non_lesion 62 Eczema CD45N Lower_back Female S26
SKN8090526 adult Dermis non_lesion 62 Eczema Live_single_spike Lower_back Female S27
SKN8090527 adult Dermis non_lesion 62 Eczema CD45N Lower_back Female S28
SKN8090528 adult Epidermis lesion 62 Eczema CD45P Lower_back Female S29
SKN8090529 adult Epidermis lesion 62 Eczema CD45N Lower_back Female S30
SKN8090530 adult Dermis lesion 62 Eczema CD45P Lower_back Female S31
SKN8090531 adult Dermis lesion 62 Eczema CD45N Lower_back Female S32
SKN8090536 adult Dermis non_lesion 50 Eczema CD45P Lower_back Male S33
SKN8090537 adult Dermis non_lesion 50 Eczema CD45N Lower_back Male S34
SKN8090538 adult Epidermis non_lesion 50 Eczema CD45P Lower_back Male S35
SKN8090539 adult Epidermis non_lesion 50 Eczema CD45N Lower_back Male S36
SKN8090540 adult Dermis lesion 50 Eczema CD45P Lower_back Male S37
SKN8090541 adult Dermis lesion 50 Eczema CD45N Lower_back Male S38
SKN8090542 adult Epidermis lesion 50 Eczema CD45P Lower_back Male S39
SKN8090543 adult Epidermis lesion 50 Eczema CD45N Lower_back Male S40
SKN8090548 adult Dermis non_lesion 61 Eczema CD45P Lower_back Male S41
SKN8090549 adult Dermis non_lesion 61 Eczema CD45N Lower_back Male S42
SKN8090550 adult Epidermis non_lesion 61 Eczema CD45P Lower_back Male S43
SKN8090551 adult Epidermis non_lesion 61 Eczema CD45N Lower_back Male S44
SKN8090552 adult Dermis lesion 61 Eczema CD45P Lower_back Male S45
SKN8090553 adult Dermis lesion 61 Eczema CD45N Lower_back Male S46
SKN8090554 adult Epidermis lesion 61 Eczema CD45P Lower_back Male S47
SKN8090555 adult Epidermis lesion 61 Eczema CD45N Lower_back Male S48
SKN8090560 adult Epidermis lesion 20 Eczema Live_single Lower_back Male S49
SKN8090561 adult Dermis lesion 20 Eczema Live_single Lower_back Male S50
SKN8090562 adult Epidermis non_lesion 20 Eczema Live_single Lower_back Male S51
SKN8090563 adult Dermis non_lesion 20 Eczema Live_single Lower_back Male S52
SKN8090564 adult Epidermis lesion 20 Eczema Live_single Lower_back Male S53
SKN8090565 adult Dermis lesion 20 Eczema Live_single Lower_back Male S54
SKN8090566 adult Epidermis non_lesion 20 Eczema Live_single Lower_back Male S55
SKN8090567 adult Dermis non_lesion 20 Eczema Live_single Lower_back Male S56
SKN8090576 adult Dermis lesion 37 Psoriasis CD45P Lower_back Female S57
SKN8090577 adult Dermis lesion 37 Psoriasis CD45N Lower_back Female S58
SKN8090578 adult Epidermis lesion 37 Psoriasis CD45P Lower_back Female S59
SKN8090579 adult Epidermis lesion 37 Psoriasis CD45N Lower_back Female S60
SKN8090580 adult Dermis non_lesion 37 Psoriasis CD45P Lower_back Female S61
SKN8090581 adult Dermis non_lesion 37 Psoriasis CD45N Lower_back Female S62
SKN8090582 adult Epidermis non_lesion 37 Psoriasis CD45P Lower_back Female S63
SKN8090583 adult Epidermis non_lesion 37 Psoriasis CD45N Lower_back Female S64
SKN8090588 adult Dermis lesion 65 Psoriasis CD45P Lower_back Male S65
SKN8090589 adult Dermis lesion 65 Psoriasis CD45N Lower_back Male S66
SKN8090590 adult Epidermis lesion 65 Psoriasis CD45P Lower_back Male S67
SKN8090591 adult Epidermis lesion 65 Psoriasis CD45N Lower_back Male S68
SKN8090592 adult Dermis non_lesion 65 Psoriasis CD45P Lower_back Male S69
SKN8090593 adult Dermis non_lesion 65 Psoriasis CD45N Lower_back Male S70
SKN8090594 adult Epidermis non_lesion 65 Psoriasis CD45P Lower_back Male S71
SKN8090595 adult Epidermis non_lesion 65 Psoriasis CD45N Lower_back Male S72
SKN8090600 adult Dermis non_lesion 62 Psoriasis CD45P Lower_back Female S73
SKN8090601 adult Dermis non_lesion 62 Psoriasis CD45N Lower_back Female S74
SKN8090602 adult Epidermis non_lesion 62 Psoriasis CD45P Lower_back Female S75
SKN8090603 adult Epidermis non_lesion 62 Psoriasis CD45N Lower_back Female S76
SKN8090604 adult Dermis lesion 62 Psoriasis CD45P Lower_back Female S77
SKN8090605 adult Dermis lesion 62 Psoriasis CD45N Lower_back Female S78
SKN8090606 adult Epidermis lesion 62 Psoriasis CD45P Lower_back Female S79
SKN8090607 adult Epidermis lesion 62 Psoriasis CD45N Lower_back Female S80
SKN8104894 adult Epidermis non_lesion Unknown Healthy CD49fN_KC Breast Female S81
SKN8104895 adult Epidermis non_lesion Unknown Healthy CD49fP_KC Breast Female S82
SKN8104896 adult Epidermis non_lesion Unknown Healthy Lymphocytes Breast Female S83
SKN8104897 adult Epidermis non_lesion Unknown Healthy APCs Breast Female S84
SKN8104899 adult Dermis non_lesion Unknown Healthy Fibroblasts Breast Female S85
SKN8104900 adult Dermis non_lesion Unknown Healthy Endothelium Breast Female S86
SKN8104901 adult Dermis non_lesion Unknown Healthy APCs Breast Female S87
SKN8104902 adult Dermis non_lesion Unknown Healthy Lymphocytes Breast Female S88
SKN8105192 adult Epidermis non_lesion Unknown Healthy CD49fN_KC Breast Female S89
SKN8105193 adult Epidermis non_lesion Unknown Healthy CD49fP_KC Breast Female S90
SKN8105194 adult Epidermis non_lesion Unknown Healthy Lymphocytes Breast Female S91
SKN8105195 adult Epidermis non_lesion Unknown Healthy APCs Breast Female S92
SKN8105197 adult Dermis non_lesion Unknown Healthy Fibroblasts Breast Female S93
SKN8105198 adult Dermis non_lesion Unknown Healthy Endothelium Breast Female S94
SKN8105199 adult Dermis non_lesion Unknown Healthy APCs Breast Female S95
SKN8105200 adult Dermis non_lesion Unknown Healthy Lymphocytes Breast Female S96

3.1.2 Cells & Genes (RNA)

sample_id pre_qc_gene pre_qc_cell post_qc_gene post_qc_cell
S1 21,214 3,525 17,443 3,173
S2 19,759 5,509 16,391 5,239
S3 20,589 7,434 17,308 7,181
S4 20,334 4,637 16,761 3,767
S5 18,914 3,825 15,026 2,666
S6 20,980 11,807 17,713 10,680
S7 20,826 7,820 16,922 6,297
S8 20,090 5,109 16,523 4,819
S9 20,779 3,916 17,554 3,858
S10 19,785 3,125 16,507 3,103
S11 20,150 4,261 16,944 4,230
S12 20,443 4,546 17,174 4,384
S13 15,826 568 12,358 497
S14 19,721 4,527 16,550 4,309
S15 18,686 3,115 15,391 3,000
S16 19,366 4,054 16,051 3,944
S17 19,984 2,382 16,707 2,364
S18 18,976 2,459 15,722 2,448
S19 18,965 2,696 15,899 2,664
S20 17,865 1,781 14,580 1,697
S21 17,865 1,780 14,553 1,579
S22 17,920 1,975 14,797 1,817
S23 18,344 2,709 15,300 2,653
S24 17,755 2,197 14,591 2,151
S25 17,389 4,186 14,339 4,185
S26 18,450 1,551 15,245 1,443
S27 9,303 88 5,090 88
S28 20,407 5,225 16,982 4,977
S29 15,424 1,202 12,511 1,201
S30 19,035 1,405 15,601 1,373
S31 17,125 2,683 14,106 2,669
S32 21,501 2,457 18,018 2,290
S33 10,396 256 7,081 256
S34 19,651 8,467 16,909 8,326
S35 19,786 7,487 16,824 7,458
S36 15,030 595 11,866 591
S37 16,451 2,267 13,807 2,261
S38 12,359 165 9,652 164
S39 19,601 8,352 16,669 8,319
S40 21,297 7,651 18,255 7,620
S41 16,221 1,622 13,422 1,606
S42 19,370 7,113 16,431 6,533
S43 20,352 6,909 17,203 6,824
S44 21,202 6,114 18,178 5,875
S45 20,216 8,299 17,247 8,035
S46 19,978 5,396 17,111 5,091
S47 20,005 7,451 16,886 7,331
S48 23,789 7,838 20,519 7,320
S49 15,291 1,628 12,380 1,628
S50 16,621 1,581 13,445 1,572
S51 11,420 284 7,679 284
S52 18,666 2,140 15,339 2,121
S53 20,003 3,888 17,001 3,852
S54 16,676 1,249 13,374 1,243
S55 11,033 320 7,585 320
S56 16,204 2,666 13,216 2,651
S57 18,506 5,397 15,545 5,376
S58 22,207 7,461 18,901 7,420
S59 14,975 975 11,872 972
S60 19,797 5,322 16,850 5,235
S61 18,110 1,990 14,949 1,987
S62 21,947 7,664 18,776 7,642
S63 14,390 1,533 11,836 1,486
S64 18,818 8,228 15,990 8,123
S65 20,103 11,587 17,146 11,521
S66 23,483 9,463 20,302 9,377
S67 16,773 887 13,829 841
S68 20,629 6,665 17,675 6,492
S69 20,877 5,494 17,782 5,452
S70 20,300 11,009 17,241 10,999
S71 14,642 691 12,013 680
S72 19,482 7,131 16,556 7,094
S73 16,581 1,511 13,622 1,501
S74 20,966 7,656 17,779 7,550
S75 15,544 822 12,870 789
S76 20,348 12,514 17,296 12,266
S77 19,515 5,392 16,379 5,344
S78 22,502 9,702 19,234 9,567
S79 16,889 1,035 13,664 969
S80 18,433 7,191 15,615 7,177
S81 20,565 6,292 17,320 5,530
S82 18,956 5,365 15,983 5,053
S83 19,648 8,600 16,613 8,508
S84 19,551 6,450 16,430 5,584
S85 21,669 6,649 18,326 6,516
S86 19,698 7,932 16,758 7,900
S87 19,523 4,950 16,391 4,575
S88 18,698 4,254 15,795 4,220
S89 20,433 5,162 16,745 4,156
S90 20,180 6,070 16,798 5,408
S91 19,804 5,171 16,665 5,078
S92 20,582 6,911 17,295 6,069
S93 21,509 5,412 17,848 4,927
S94 20,281 8,028 17,256 7,983
S95 20,022 7,869 17,096 7,412
S96 20,600 4,866 17,382 4,677

3.1.3 UMI per cell (RNA)

Vales are post-QC.

sample_id min 0% 25% 50% 75% 100% max
S1 1,008 1,008 4,587 7,297 10,510 43,734 43,734
S2 1,001 1,001 2,228 2,939 3,705 28,934 28,934
S3 1,004 1,004 5,381 7,338 9,553 34,584 34,584
S4 1,002 1,002 4,872 7,159 9,052 27,889 27,889
S5 1,000 1,000 2,473 6,233 10,190 31,650 31,650
S6 1,005 1,005 5,610 7,960 10,599 38,428 38,428
S7 1,007 1,007 5,119 7,142 9,225 52,283 52,283
S8 1,007 1,007 2,237 2,885 3,772 28,865 28,865
S9 1,001 1,001 3,688 5,972 8,762 39,803 39,803
S10 1,002 1,002 2,602 3,376 4,484 33,684 33,684
S11 1,021 1,021 5,213 7,264 9,782 43,327 43,327
S12 1,002 1,002 4,442 7,428 9,830 46,737 46,737
S13 1,000 1,000 5,787 10,631 15,084 29,104 29,104
S14 1,015 1,015 7,262 11,073 14,733 42,806 42,806
S15 1,003 1,003 6,361 8,555 10,594 47,848 47,848
S16 1,004 1,004 2,818 3,455 4,303 38,577 38,577
S17 1,020 1,020 4,190 6,584 10,127 40,002 40,002
S18 1,010 1,010 2,232 2,759 3,521 40,226 40,226
S19 1,013 1,013 5,562 7,534 9,741 29,171 29,171
S20 1,002 1,002 3,327 6,962 9,398 31,690 31,690
S21 1,013 1,013 6,590 9,866 13,897 52,224 52,224
S22 1,000 1,000 5,269 8,756 12,495 43,764 43,764
S23 1,002 1,002 4,056 6,429 8,468 54,392 54,392
S24 1,002 1,002 2,463 3,084 3,826 29,264 29,264
S25 999 999 2,701 4,234 5,668 15,105 15,105
S26 1,016 1,016 9,018 18,893 27,705 101,400 101,400
S27 962 962 1,172 1,412 1,674 4,429 4,429
S28 1,001 1,001 2,529 3,613 5,109 28,534 28,534
S29 1,002 1,002 1,726 2,467 4,558 11,850 11,850
S30 1,028 1,028 5,143 8,870 13,124 45,596 45,596
S31 799 799 1,471 2,075 3,386 15,413 15,413
S32 1,007 1,007 4,685 8,358 13,992 75,079 75,079
S33 993 993 1,676 2,515 3,305 6,815 6,815
S34 1,001 1,001 4,369 8,356 12,218 45,826 45,826
S35 754 754 2,650 3,576 5,964 32,177 32,177
S36 996 996 1,082 1,333 3,750 15,572 15,572
S37 1,004 1,004 2,949 5,243 7,189 21,634 21,634
S38 1,582 1,582 6,044 8,627 11,911 26,947 26,947
S39 971 971 2,736 3,797 6,117 27,988 27,988
S40 967 967 2,969 5,032 7,366 33,325 33,325
S41 1,005 1,005 2,491 4,239 8,317 29,082 29,082
S42 1,001 1,001 4,899 9,084 13,571 44,176 44,176
S43 831 831 3,030 4,300 7,311 39,966 39,966
S44 1,000 1,000 4,458 6,519 9,171 41,706 41,706
S45 751 751 3,127 5,555 12,512 46,942 46,942
S46 1,011 1,011 9,752 15,208 22,026 68,048 68,048
S47 758 758 2,644 3,858 7,096 41,541 41,541
S48 1,002 1,002 6,884 10,820 15,360 51,191 51,191
S49 998 998 1,305 1,689 2,281 9,767 9,767
S50 785 785 1,554 2,148 3,132 16,031 16,031
S51 986 986 1,091 1,252 1,507 3,207 3,207
S52 850 850 3,134 4,650 6,900 33,768 33,768
S53 1,019 1,019 4,598 8,239 11,046 33,725 33,725
S54 846 846 1,852 2,649 3,834 14,396 14,396
S55 991 991 1,104 1,264 1,521 4,247 4,247
S56 1,000 1,000 1,328 1,755 2,360 11,739 11,739
S57 759 759 1,837 2,434 4,228 24,475 24,475
S58 1,002 1,002 3,731 5,790 8,544 40,684 40,684
S59 997 997 1,336 1,758 3,128 18,930 18,930
S60 1,005 1,005 5,246 10,365 17,037 56,885 56,885
S61 795 795 2,266 3,126 6,656 28,129 28,129
S62 1,001 1,001 3,722 5,778 8,277 30,502 30,502
S63 996 996 5,430 6,531 7,646 22,373 22,373
S64 1,003 1,003 6,234 8,152 10,005 40,735 40,735
S65 754 754 2,311 3,189 6,144 35,677 35,677
S66 1,002 1,002 4,467 7,333 11,212 84,775 84,775
S67 1,000 1,000 2,597 4,060 8,205 90,696 90,696
S68 1,011 1,011 11,220 19,506 29,734 103,777 103,777
S69 755 755 3,732 5,220 11,937 49,043 49,043
S70 1,000 1,000 1,555 2,117 3,050 15,460 15,460
S71 1,396 1,396 10,373 12,548 15,184 31,110 31,110
S72 1,003 1,003 7,520 11,088 14,526 63,076 63,076
S73 1,002 1,002 1,676 2,439 4,527 20,924 20,924
S74 1,002 1,002 2,466 3,548 5,559 25,549 25,549
S75 1,159 1,159 8,381 14,037 18,720 58,248 58,248
S76 1,004 1,004 6,180 8,640 11,517 45,466 45,466
S77 1,009 1,009 2,705 3,528 5,459 37,650 37,650
S78 1,001 1,001 3,081 4,840 7,624 56,265 56,265
S79 1,000 1,000 2,639 3,826 6,113 56,647 56,647
S80 1,004 1,004 2,786 4,094 5,643 18,087 18,087
S81 1,011 1,011 8,388 12,096 15,452 56,817 56,817
S82 1,007 1,007 5,698 7,780 9,927 38,023 38,023
S83 1,002 1,002 2,907 3,712 4,687 50,071 50,071
S84 1,001 1,001 7,300 10,320 13,490 44,469 44,469
S85 1,003 1,003 5,428 8,643 13,146 42,937 42,937
S86 994 994 4,040 5,412 6,884 27,334 27,334
S87 1,006 1,006 3,674 6,277 9,144 27,742 27,742
S88 1,002 1,002 2,158 2,700 3,387 25,847 25,847
S89 1,007 1,007 2,978 6,236 12,803 46,017 46,017
S90 1,000 1,000 4,590 7,806 10,922 54,701 54,701
S91 1,006 1,006 3,816 4,840 5,991 77,369 77,369
S92 1,003 1,003 10,271 15,225 20,231 61,873 61,873
S93 1,003 1,003 5,560 7,918 10,870 42,313 42,313
S94 1,011 1,011 6,966 8,710 10,893 41,565 41,565
S95 1,005 1,005 5,090 8,414 11,552 32,846 32,846
S96 1,008 1,008 3,986 5,019 6,145 42,404 42,404

3.1.4 Gene per cell (RNA)

Vales are post-QC.

sample_id min 0% 25% 50% 75% 100% max
S1 460 460 1,502 2,072 2,696 5,419 5,419
S2 429 429 868 1,046 1,241 5,376 5,376
S3 485 485 1,664 2,124 2,606 5,321 5,321
S4 443 443 1,446 1,796 2,136 4,856 4,856
S5 402 402 843 1,336 1,948 4,439 4,439
S6 432 432 1,335 1,704 2,181 5,230 5,230
S7 439 439 1,342 1,624 1,943 5,322 5,322
S8 401 401 759 962 1,241 4,658 4,658
S9 415 415 1,240 1,722 2,278 5,145 5,145
S10 400 400 896 1,073 1,330 5,225 5,225
S11 480 480 1,501 1,976 2,475 5,248 5,248
S12 404 404 1,157 1,504 1,830 5,931 5,931
S13 421 421 1,206 1,734 2,305 3,615 3,615
S14 442 442 1,572 2,065 2,599 5,148 5,148
S15 424 424 1,412 1,697 2,004 5,053 5,053
S16 409 409 907 1,100 1,332 4,733 4,733
S17 440 440 1,331 1,850 2,470 5,083 5,083
S18 442 442 816 980 1,196 5,129 5,129
S19 420 420 1,530 1,978 2,523 4,766 4,766
S20 405 405 1,030 1,371 1,662 4,967 4,967
S21 406 406 1,224 1,661 2,219 4,782 4,782
S22 449 449 1,320 1,792 2,239 4,884 4,884
S23 407 407 1,132 1,471 1,782 4,529 4,529
S24 417 417 798 1,023 1,250 4,224 4,224
S25 405 405 875 1,088 1,306 2,553 2,553
S26 410 410 2,282 2,831 3,303 5,538 5,538
S27 388 388 594 658 756 1,507 1,507
S28 412 412 1,108 1,464 1,845 4,385 4,385
S29 411 411 792 992 1,314 2,933 2,933
S30 405 405 1,591 2,100 2,624 4,469 4,469
S31 389 389 626 823 1,071 2,884 2,884
S32 449 449 1,478 2,159 2,900 5,928 5,928
S33 409 409 569 766 932 1,631 1,631
S34 403 403 1,152 1,636 2,069 4,745 4,745
S35 304 304 891 1,171 1,515 4,380 4,380
S36 440 440 570 657 1,132 3,232 3,232
S37 403 403 907 1,188 1,477 3,176 3,176
S38 459 459 1,369 1,680 2,078 3,569 3,569
S39 412 412 944 1,201 1,562 4,520 4,520
S40 410 410 1,048 1,480 1,963 4,705 4,705
S41 426 426 894 1,236 1,618 3,114 3,114
S42 420 420 1,387 1,936 2,423 4,763 4,763
S43 396 396 1,045 1,370 1,860 5,571 5,571
S44 430 430 1,419 1,862 2,346 5,439 5,439
S45 401 401 1,000 1,463 2,007 4,960 4,960
S46 405 405 2,148 2,676 3,236 5,656 5,656
S47 401 401 874 1,162 1,630 5,171 5,171
S48 434 434 1,972 2,619 3,315 5,986 5,986
S49 411 411 615 724 871 1,985 1,985
S50 400 400 676 847 1,109 3,084 3,084
S51 399 399 526 590 686 1,155 1,155
S52 399 399 1,209 1,605 2,098 4,429 4,429
S53 477 477 1,542 2,016 2,352 5,013 5,013
S54 403 403 784 1,033 1,338 2,934 2,934
S55 400 400 556 618 704 1,134 1,134
S56 410 410 624 770 963 2,798 2,798
S57 358 358 743 920 1,225 4,418 4,418
S58 416 416 1,271 1,726 2,289 5,073 5,073
S59 399 399 569 764 1,004 3,050 3,050
S60 406 406 1,348 1,989 2,537 4,502 4,502
S61 412 412 960 1,199 1,683 4,314 4,314
S62 424 424 1,303 1,790 2,294 5,751 5,751
S63 447 447 1,230 1,402 1,555 3,089 3,089
S64 439 439 1,413 1,661 1,928 4,744 4,744
S65 324 324 843 1,098 1,481 4,687 4,687
S66 420 420 1,429 1,983 2,651 5,819 5,819
S67 429 429 821 1,113 1,659 5,347 5,347
S68 424 424 2,121 2,920 3,500 5,995 5,995
S69 366 366 1,365 1,678 2,147 5,800 5,800
S70 405 405 674 845 1,103 3,435 3,435
S71 457 457 1,888 2,163 2,428 3,887 3,887
S72 434 434 1,850 2,208 2,555 5,314 5,314
S73 425 425 797 1,067 1,499 3,982 3,982
S74 424 424 1,030 1,385 1,828 4,593 4,593
S75 469 469 1,735 2,319 2,766 5,191 5,191
S76 411 411 1,429 1,709 2,044 4,725 4,725
S77 408 408 902 1,160 1,507 4,776 4,776
S78 401 401 1,057 1,438 1,944 5,348 5,348
S79 416 416 940 1,378 1,917 5,277 5,277
S80 400 400 896 1,171 1,419 3,085 3,085
S81 426 426 1,841 2,232 2,624 5,199 5,199
S82 440 440 1,455 1,758 2,056 4,536 4,536
S83 413 413 1,099 1,372 1,650 4,771 4,771
S84 435 435 1,474 1,902 2,358 5,116 5,116
S85 451 451 1,788 2,434 3,060 5,936 5,936
S86 403 403 1,501 1,884 2,253 4,664 4,664
S87 409 409 1,277 1,716 2,104 4,217 4,217
S88 444 444 995 1,161 1,366 4,959 4,959
S89 411 411 1,137 1,698 2,317 4,986 4,986
S90 406 406 1,331 1,789 2,203 5,314 5,314
S91 434 434 1,427 1,714 2,000 5,229 5,229
S92 409 409 1,796 2,384 2,935 5,411 5,411
S93 421 421 1,784 2,304 2,840 5,493 5,493
S94 449 449 2,263 2,674 3,068 5,949 5,949
S95 414 414 1,596 2,062 2,447 4,541 4,541
S96 419 419 1,648 1,930 2,223 5,848 5,848

3.1.5 Mitochondrial (%) per cell (RNA)

Vales are post-QC.

sample_id min 0% 25% 50% 75% 100% max
S1 0.00 0.00 3.96 5.25 6.66 10.00 10.00
S2 0.00 0.00 3.18 4.63 6.15 9.98 9.98
S3 0.00 0.00 2.95 4.13 5.26 9.98 9.98
S4 0.00 0.00 3.48 5.09 6.78 10.00 10.00
S5 0.03 0.03 4.33 6.08 7.70 10.00 10.00
S6 0.00 0.00 3.42 4.54 5.98 10.00 10.00
S7 0.00 0.00 4.29 5.89 7.51 10.00 10.00
S8 0.00 0.00 2.42 3.69 5.15 9.96 9.96
S9 0.00 0.00 1.52 2.14 3.01 9.96 9.96
S10 0.00 0.00 1.87 2.57 3.45 9.75 9.75
S11 0.00 0.00 1.28 1.84 2.43 9.89 9.89
S12 0.00 0.00 1.66 2.61 3.82 9.91 9.91
S13 0.00 0.00 2.20 3.29 4.47 9.91 9.91
S14 0.00 0.00 1.55 2.24 3.12 9.94 9.94
S15 0.00 0.00 2.20 3.15 4.18 9.98 9.98
S16 0.00 0.00 1.99 2.73 3.58 9.92 9.92
S17 0.00 0.00 1.42 1.95 2.65 9.78 9.78
S18 0.00 0.00 1.75 2.44 3.33 9.74 9.74
S19 0.00 0.00 1.07 1.48 1.98 9.49 9.49
S20 0.00 0.00 1.51 2.21 3.23 9.96 9.96
S21 0.00 0.00 1.73 2.61 3.61 9.96 9.96
S22 0.00 0.00 1.29 1.98 2.97 9.96 9.96
S23 0.00 0.00 1.24 2.09 3.46 9.65 9.65
S24 0.00 0.00 1.11 1.86 2.75 9.91 9.91
S25 0.00 0.00 0.80 1.15 1.74 9.60 9.60
S26 0.00 0.00 1.51 2.29 3.59 9.88 9.88
S27 0.22 0.22 1.27 1.78 2.29 9.15 9.15
S28 0.00 0.00 2.63 3.63 4.71 10.00 10.00
S29 0.00 0.00 1.58 2.34 3.15 8.18 8.18
S30 0.06 0.06 1.32 2.07 3.20 9.87 9.87
S31 0.00 0.00 1.40 2.24 3.12 9.03 9.03
S32 0.00 0.00 1.57 2.54 3.89 9.99 9.99
S33 0.00 0.00 0.25 0.51 0.78 4.02 4.02
S34 0.00 0.00 0.47 0.98 1.74 9.99 9.99
S35 0.00 0.00 0.47 1.05 1.96 9.88 9.88
S36 0.00 0.00 1.25 1.71 2.10 9.07 9.07
S37 0.00 0.00 0.25 0.48 0.93 9.98 9.98
S38 0.00 0.00 0.42 0.98 1.89 7.65 7.65
S39 0.00 0.00 0.25 0.64 1.39 9.88 9.88
S40 0.00 0.00 0.38 0.79 1.54 9.89 9.89
S41 0.00 0.00 1.01 2.02 3.01 9.63 9.63
S42 0.00 0.00 1.14 1.97 3.35 9.99 9.99
S43 0.00 0.00 1.31 2.18 3.31 9.87 9.87
S44 0.00 0.00 1.59 2.44 3.63 9.98 9.98
S45 0.00 0.00 0.95 1.65 2.68 10.00 10.00
S46 0.00 0.00 1.37 2.12 3.38 10.00 10.00
S47 0.00 0.00 1.41 2.13 3.15 9.97 9.97
S48 0.00 0.00 1.27 2.07 3.25 10.00 10.00
S49 0.00 0.00 1.18 1.55 2.01 7.08 7.08
S50 0.24 0.24 1.19 1.58 2.08 9.03 9.03
S51 0.24 0.24 1.05 1.35 1.77 3.23 3.23
S52 0.00 0.00 1.48 1.94 2.50 9.95 9.95
S53 0.00 0.00 1.94 2.74 3.65 9.90 9.90
S54 0.00 0.00 1.20 1.76 2.34 8.16 8.16
S55 0.19 0.19 1.12 1.50 1.93 4.84 4.84
S56 0.16 0.16 1.22 1.58 1.99 9.69 9.69
S57 0.00 0.00 0.42 1.24 2.24 9.82 9.82
S58 0.00 0.00 0.48 1.42 2.72 9.98 9.98
S59 0.00 0.00 0.07 0.22 0.56 7.96 7.96
S60 0.00 0.00 0.35 0.87 1.82 9.99 9.99
S61 0.00 0.00 0.20 0.52 1.55 9.64 9.64
S62 0.00 0.00 0.28 0.74 1.93 9.92 9.92
S63 0.00 0.00 1.73 2.54 3.30 9.92 9.92
S64 0.00 0.00 2.12 3.17 4.41 9.92 9.92
S65 0.00 0.00 0.10 0.22 0.44 9.33 9.33
S66 0.00 0.00 0.25 0.52 1.28 9.91 9.91
S67 0.00 0.00 0.44 0.91 1.74 9.96 9.96
S68 0.00 0.00 0.30 0.62 1.31 9.95 9.95
S69 0.00 0.00 0.44 1.09 2.15 9.88 9.88
S70 0.00 0.00 0.46 1.21 2.23 9.88 9.88
S71 0.00 0.00 1.89 3.71 4.47 8.77 8.77
S72 0.00 0.00 1.00 1.95 2.94 9.85 9.85
S73 0.00 0.00 1.63 2.82 4.08 9.43 9.43
S74 0.00 0.00 1.21 2.16 3.36 9.99 9.99
S75 0.00 0.00 1.66 2.27 3.05 8.86 8.86
S76 0.00 0.00 1.60 2.45 3.41 9.86 9.86
S77 0.00 0.00 0.83 1.50 2.42 9.83 9.83
S78 0.00 0.00 1.10 1.85 2.88 9.99 9.99
S79 0.00 0.00 0.19 0.57 1.16 9.99 9.99
S80 0.00 0.00 0.53 0.97 1.68 9.80 9.80
S81 0.00 0.00 2.71 3.80 5.04 9.98 9.98
S82 0.00 0.00 2.68 3.92 5.19 9.97 9.97
S83 0.00 0.00 1.73 2.72 3.76 9.80 9.80
S84 0.00 0.00 2.66 3.80 5.07 10.00 10.00
S85 0.00 0.00 1.94 2.62 3.49 9.92 9.92
S86 0.00 0.00 1.54 2.19 2.92 9.86 9.86
S87 0.00 0.00 2.08 3.21 4.61 9.98 9.98
S88 0.00 0.00 2.30 3.16 4.10 9.94 9.94
S89 0.00 0.00 2.89 4.46 6.32 10.00 10.00
S90 0.00 0.00 2.47 3.92 5.63 10.00 10.00
S91 0.00 0.00 0.90 2.82 4.43 9.99 9.99
S92 0.00 0.00 2.81 4.53 5.88 9.98 9.98
S93 0.00 0.00 3.77 5.01 6.37 10.00 10.00
S94 0.00 0.00 2.84 3.54 4.24 9.96 9.96
S95 0.00 0.00 3.65 4.68 5.79 9.99 9.99
S96 0.00 0.00 4.11 5.15 6.30 9.98 9.98


3.2 Distribution Plots for Quality Control Metrics

Thresholds, represented by dashed lines, were implemented to filter the data and only retain cells of high quality.

3.2.1 UMI per cell

3.2.2 Gene per cell

3.2.3 Mitochondrial (%) per cell


3.3 Barcodes contamination

3.3.1 Raw count

Number of barcodes shared between pairs of samples post-QC.

## [1] "No overlaps among samples' barcodes."

3.3.2 Jaccard Index

Fraction (%) of barcodes shared between pairs of samples post-QC.

## [1] "No overlaps among samples' barcodes."


3.4 Impact of Quality Control on Cell, Gene, and UMI Abundances

3.4.1 Number of cells and genes per sample

diamonds and diamonds refer to before and after QC, respectively.

3.4.2 Average number of UMIs/cell and genes/cell per sample

The error bars represent the standard deviation of the number of UMIs and genes across cells per sample.


3.5 Key QC Metrics of Merged Samples

min 0% 25% 50% 75% 100% max
UMI per cell 751 751 3,197 5,824 9,824 103,777 103,777
Gene per cell 304 304 1,098 1,591 2,181 5,995 5,995
Mitochondrial (%) per cell 0.00 0.00 1.07 2.24 3.82 10.00 10.00

3.6 Visualization of Merged scRNA-Seq Object in 2D Space

Note: Labels may have been removed if they overlap excessively.

3.6.1 Signacx SPRING Projection

3.6.2 Seurat UMAP Projection

3.6.3 Seurat UMAP Projection (no-batch correction)


3.7 Visualizing Cell QC Metrics Using Dimensionality Reduction

Note: QC metrics based on kernel density estimation.

3.7.1 UMI per cell - SPRING Projection

3.7.2 Gene per cell - SPRING Projection

3.7.3 Mitochondrial (%) per cell - SPRING Projection

3.7.4 UMI per cell - UMAP Projection

3.7.5 Gene per cell - UMAP Projection

3.7.6 Mitochondrial (%) per cell - UMAP Projection


4 BridgeCluster

Note: Labels may have been removed if they overlap excessively.

4.1 Visualizing Cell Populations with Dimensionality Reduction

4.1.1 Signacx SPRING Projection

4.1.2 Seurat UMAP Projection


4.2 Cell Cluster Composition

Values at the top of each bar indicate the percentage of cells

4.2.1 Seurat

4.2.2 Signacx


4.3 Statistical Dispersion Analysis of Cell Composition in Clusters across sample

This measurement is a proxy to batch effect artifacts. Values adjacent to each point indicate the number of cells.

4.3.1 Seurat

4.3.2 Signacx


4.4 Markers per cluster

Top 25 differentially expressed genes ( p_val_adj < 0.05 and pct.1 > 0.5 ) for each of the clusters

4.4.1 Seurat

4.4.2 Signacx


5 BridgeAnnotation

5.1 Visualizing Distinct Cell Type Populations with Dimensionality Reduction

Note: Labels may have been removed if they overlap excessively.

5.1.1 Signacx SPRING Projection

5.1.2 Signacx UMAP Projection


5.2 Cell Type Population Composition

Values at the top of each bar indicate the percentage of cells

5.2.1 Signacx


6 References

Publication: no referrence

Data Availability: no referrence


7 Session Information

This is the output of sessionInfo() on the computing system on which this document was compiled

## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## Random number generation:
##  RNG:     L'Ecuyer-CMRG 
##  Normal:  Inversion 
##  Sample:  Rejection 
##  
## locale:
## [1] C
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    grid      stats     graphics  grDevices
## [6] utils     datasets  methods   base     
## 
## other attached packages:
##  [1] edgeR_4.0.2                 limma_3.58.1               
##  [3] slingshot_2.10.0            TrajectoryUtils_1.10.0     
##  [5] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
##  [7] Biobase_2.62.0              GenomicRanges_1.54.1       
##  [9] GenomeInfoDb_1.38.1         IRanges_2.36.0             
## [11] S4Vectors_0.40.2            BiocGenerics_0.48.1        
## [13] MatrixGenerics_1.14.0       matrixStats_1.1.0          
## [15] princurve_2.1.6             Nebulosa_1.12.0            
## [17] patchwork_1.1.3             data.table_1.14.10         
## [19] ComplexHeatmap_2.18.0       visNetwork_2.1.2           
## [21] plotly_4.10.3               data.tree_1.1.0            
## [23] DT_0.30                     readxl_1.4.3               
## [25] gtools_3.9.5                gplots_3.1.3               
## [27] gridtext_0.1.5              igraph_1.5.1               
## [29] sargent_1.0.1               SignacX_2.2.5              
## [31] harmony_1.2.0               Rcpp_1.0.11                
## [33] kableExtra_1.3.4            purrr_1.0.2                
## [35] reticulate_1.34.0           RColorBrewer_1.1-3         
## [37] cowplot_1.1.1               gridExtra_2.3              
## [39] pheatmap_1.0.12             ggrepel_0.9.4              
## [41] ggplot2_3.4.4               Seurat_5.0.1               
## [43] SeuratObject_5.0.1          sp_2.1-2                   
## [45] dplyr_1.1.4                 optparse_1.7.3             
## 
## loaded via a namespace (and not attached):
##   [1] spatstat.sparse_3.0-3   bitops_1.0-7           
##   [3] httr_1.4.7              webshot_0.5.5          
##   [5] doParallel_1.0.17       tools_4.3.2            
##   [7] sctransform_0.4.1       utf8_1.2.4             
##   [9] R6_2.5.1                mgcv_1.9-0             
##  [11] lazyeval_0.2.2          uwot_0.1.16            
##  [13] ggdist_3.3.1            GetoptLong_1.0.5       
##  [15] withr_2.5.2             progressr_0.14.0       
##  [17] cli_3.6.1               spatstat.explore_3.2-5 
##  [19] fastDummies_1.7.3       labeling_0.4.3         
##  [21] sass_0.4.8              mvtnorm_1.2-4          
##  [23] spatstat.data_3.0-3     proxy_0.4-27           
##  [25] ggridges_0.5.4          pbapply_1.7-2          
##  [27] commonmark_1.9.0        systemfonts_1.0.5      
##  [29] R.utils_2.12.3          svglite_2.1.2          
##  [31] parallelly_1.36.0       rstudioapi_0.15.0      
##  [33] generics_0.1.3          shape_1.4.6            
##  [35] crosstalk_1.2.1         ica_1.0-3              
##  [37] spatstat.random_3.2-2   distributional_0.3.2   
##  [39] Matrix_1.6-4            fansi_1.0.6            
##  [41] DescTools_0.99.52       abind_1.4-5            
##  [43] R.methodsS3_1.8.2       lifecycle_1.0.4        
##  [45] yaml_2.3.7              SparseArray_1.2.2      
##  [47] Rtsne_0.17              promises_1.2.1         
##  [49] crayon_1.5.2            miniUI_0.1.1.1         
##  [51] lattice_0.22-5          pillar_1.9.0           
##  [53] knitr_1.45              rjson_0.2.21           
##  [55] boot_1.3-28.1           gld_2.6.6              
##  [57] future.apply_1.11.0     codetools_0.2-19       
##  [59] leiden_0.4.3.1          glue_1.6.2             
##  [61] vctrs_0.6.5             png_0.1-8              
##  [63] spam_2.10-0             neuralnet_1.44.2       
##  [65] cellranger_1.1.0        gtable_0.3.4           
##  [67] cachem_1.0.8            ks_1.14.1              
##  [69] xfun_0.41               S4Arrays_1.2.0         
##  [71] mime_0.12               pracma_2.4.4           
##  [73] survival_3.5-7          pbmcapply_1.5.1        
##  [75] iterators_1.0.14        statmod_1.5.0          
##  [77] ellipsis_0.3.2          fitdistrplus_1.1-11    
##  [79] ROCR_1.0-11             nlme_3.1-164           
##  [81] RcppAnnoy_0.0.21        bslib_0.6.1            
##  [83] irlba_2.3.5.1           KernSmooth_2.23-22     
##  [85] colorspace_2.1-0        Exact_3.2              
##  [87] tidyselect_1.2.0        compiler_4.3.2         
##  [89] rvest_1.0.3             expm_0.999-8           
##  [91] xml2_1.3.6              DelayedArray_0.28.0    
##  [93] scales_1.3.0            caTools_1.18.2         
##  [95] lmtest_0.9-40           stringr_1.5.1          
##  [97] digest_0.6.33           goftest_1.2-3          
##  [99] presto_1.0.0            spatstat.utils_3.0-4   
## [101] rmarkdown_2.25          RhpcBLASctl_0.23-42    
## [103] XVector_0.42.0          htmltools_0.5.7        
## [105] pkgconfig_2.0.3         highr_0.10             
## [107] fastmap_1.1.1           rlang_1.1.2            
## [109] GlobalOptions_0.1.2     htmlwidgets_1.6.4      
## [111] shiny_1.8.0             jquerylib_0.1.4        
## [113] farver_2.1.1            zoo_1.8-12             
## [115] jsonlite_1.8.8          mclust_6.0.1           
## [117] R.oo_1.25.0             RCurl_1.98-1.13        
## [119] magrittr_2.0.3          GenomeInfoDbData_1.2.11
## [121] dotCall64_1.1-1         munsell_0.5.0          
## [123] stringi_1.8.2           rootSolve_1.8.2.4      
## [125] zlibbioc_1.48.0         MASS_7.3-60            
## [127] plyr_1.8.9              parallel_4.3.2         
## [129] listenv_0.9.0           lmom_3.0               
## [131] deldir_2.0-2            splines_4.3.2          
## [133] tensor_1.5              circlize_0.4.15        
## [135] locfit_1.5-9.8          spatstat.geom_3.2-7    
## [137] markdown_1.12           RcppHNSW_0.5.0         
## [139] reshape2_1.4.4          evaluate_0.23          
## [141] foreach_1.5.2           httpuv_1.6.13          
## [143] RANN_2.6.1              tidyr_1.3.0            
## [145] getopt_1.20.4           polyclip_1.10-6        
## [147] future_1.33.0           clue_0.3-65            
## [149] scattermore_1.2         xtable_1.8-4           
## [151] e1071_1.7-14            RSpectra_0.16-1        
## [153] later_1.3.2             viridisLite_0.4.2      
## [155] class_7.3-22            tibble_3.2.1           
## [157] cluster_2.1.6           globals_0.16.2