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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 500 15 250 3 0.25 LogNormalize 1e+06 2000 30 20 0.7 sample FALSE 30 0.25 0.5 TRUE wilcox 0 FALSE none 1000 50 1.0.0

3 BridgeQC

3.1 Sample-level Characteristics and Quality Control Metrics

3.1.1 Metadata

sample disease treatment tissue sample_id
Control01 Control pre_tx Skin S1
Control02 Control pre_tx Skin S2
Control03 Control pre_tx Skin S3
Control04 Control pre_tx Skin S4
Control05 Control pre_tx Skin S5
Control06 Control pre_tx Skin S6
Control07 Control pre_tx Skin S7
Control08 Control pre_tx Skin S8
Control09 Control pre_tx Skin S9
Control10 Control pre_tx Skin S10
HIS_DIS_01M_LS_Der HS pre_tx Dermis S11
HIS_DIS_01M_LS_Epi HS pre_tx Epidermis S12
HIS_DIS_02M_LS_Der HS pre_tx Dermis S13
HIS_DIS_02M_LS_Epi HS pre_tx Epidermis S14
HIS_DIS_A_LS_Total HS pre_tx Skin S15
HIS_DIS_B_LS_Total HS pre_tx Skin S16
HIS_DIS_D_LS_Der HS pre_tx Dermis S17
HIS_DIS_D_LS_Epi HS pre_tx Epidermis S18
Psoriasis01_preTx_LS PSO pre_tx Skin S19
Psoriasis02_preTx_LS PSO pre_tx Skin S20
Psoriasis03_preTx_LS PSO pre_tx Skin S21
Psoriasis04_postTx_week12_LS PSO post_tx Skin S22
Psoriasis04_preTx_LS PSO pre_tx Skin S23
Psoriasis05_postTx_week12_LS PSO post_tx Skin S24
Psoriasis05_preTx_LS PSO pre_tx Skin S25
Psoriasis06_preTx_LS PSO pre_tx Skin S26
Psoriasis07_postTx_week12_LS PSO post_tx Skin S27
Psoriasis07_postTx_week48_LS PSO post_tx Skin S28
Psoriasis07_preTx_LS PSO pre_tx Skin S29
Psoriasis07_preTx_LS_02 PSO pre_tx Skin S30
Psoriasis07_preTx_NL_02 PSO pre_tx Skin S31
Psoriasis08_postTx_week12_LS PSO post_tx Skin S32
Psoriasis08_postTx_week24_LS PSO post_tx Skin S33
Psoriasis08_preTx_LS PSO pre_tx Skin S34
Psoriasis09_preTx_LS PSO pre_tx Skin S35
Psoriasis10_preTx_LS PSO pre_tx Skin S36

3.1.2 Cells & Genes (RNA)

sample_id pre_qc_gene pre_qc_cell post_qc_gene post_qc_cell
S1 21,046 2,582 17,315 2,454
S2 19,744 1,033 15,451 739
S3 15,547 355 10,924 303
S4 21,850 1,531 17,718 1,383
S5 13,251 281 8,570 72
S6 21,133 1,171 16,223 549
S7 19,574 839 15,628 586
S8 21,223 3,871 17,080 2,628
S9 21,009 2,615 17,269 2,289
S10 20,577 2,490 16,298 1,406
S11 23,312 3,301 19,486 2,660
S12 22,912 3,564 18,718 1,939
S13 20,118 906 15,771 653
S14 20,728 1,423 16,241 660
S15 21,731 1,855 17,776 1,578
S16 22,167 2,308 18,079 1,967
S17 20,513 1,867 16,391 1,524
S18 20,106 1,229 15,956 1,013
S19 19,032 945 15,298 735
S20 19,041 969 15,503 902
S21 19,899 1,432 16,488 1,256
S22 20,355 1,761 16,842 1,626
S23 20,857 2,187 17,213 1,991
S24 17,948 705 14,312 672
S25 21,962 2,894 18,350 2,749
S26 21,283 1,989 17,631 1,773
S27 22,710 2,575 18,492 1,533
S28 20,863 1,159 16,573 884
S29 21,976 1,738 17,973 1,282
S30 22,644 2,469 18,464 1,808
S31 21,774 2,026 17,359 906
S32 20,914 1,515 16,258 729
S33 23,576 4,333 19,449 2,571
S34 24,304 4,340 20,482 2,733
S35 22,437 2,168 18,375 1,117
S36 22,486 1,855 18,368 1,410

3.1.3 UMI per cell (RNA)

Vales are post-QC.

sample_id min 0% 25% 50% 75% 100% max
S1 502 502 2,120 6,262 15,019 85,792 85,792
S2 500 500 975 1,856 4,142 64,248 64,248
S3 502 502 1,072 2,639 6,558 80,478 80,478
S4 503 503 1,060 2,589 5,510 65,620 65,620
S5 500 500 967 2,954 4,753 42,003 42,003
S6 518 518 1,935 4,576 15,689 173,961 173,961
S7 503 503 1,848 6,046 19,214 130,639 130,639
S8 500 500 1,025 2,358 9,111 128,956 128,956
S9 501 501 1,355 3,137 7,638 248,954 248,954
S10 500 500 1,403 4,256 13,214 89,594 89,594
S11 500 500 3,504 4,818 8,560 125,738 125,738
S12 505 505 2,974 5,509 14,722 135,798 135,798
S13 503 503 3,372 5,215 7,631 182,243 182,243
S14 502 502 2,038 4,830 11,952 209,579 209,579
S15 520 520 3,493 4,634 6,543 98,359 98,359
S16 500 500 3,674 4,777 6,572 136,848 136,848
S17 506 506 2,910 3,795 4,991 116,660 116,660
S18 505 505 3,464 4,617 6,292 110,581 110,581
S19 505 505 2,411 3,454 4,729 76,643 76,643
S20 502 502 1,786 4,204 9,365 55,775 55,775
S21 528 528 2,485 4,126 11,370 118,279 118,279
S22 503 503 1,539 3,480 9,551 59,279 59,279
S23 505 505 2,060 3,049 7,622 42,729 42,729
S24 500 500 963 1,459 3,759 25,284 25,284
S25 500 500 2,001 2,992 9,034 94,985 94,985
S26 511 511 2,426 3,341 10,990 42,965 42,965
S27 508 508 2,682 4,875 15,684 98,238 98,238
S28 506 506 3,192 4,598 10,552 84,953 84,953
S29 510 510 2,917 4,176 13,739 112,848 112,848
S30 552 552 3,040 5,243 18,197 117,307 117,307
S31 512 512 3,909 9,194 22,492 83,035 83,035
S32 523 523 3,308 7,507 16,600 99,133 99,133
S33 501 501 2,714 6,173 15,362 198,545 198,545
S34 506 506 3,582 5,318 16,124 238,213 238,213
S35 517 517 3,300 7,073 21,424 134,496 134,496
S36 513 513 2,782 5,067 11,473 212,095 212,095

3.1.4 Gene per cell (RNA)

Vales are post-QC.

sample_id min 0% 25% 50% 75% 100% max
S1 253 253 764 1,486 2,418 7,088 7,088
S2 251 251 471 745 1,362 8,316 8,316
S3 255 255 432 871 1,554 6,540 6,540
S4 250 250 495 895 1,588 7,399 7,399
S5 268 268 475 1,190 1,767 3,996 3,996
S6 251 251 767 1,537 2,860 9,266 9,266
S7 261 261 722 1,755 3,212 8,450 8,450
S8 253 253 517 872 1,948 6,794 6,794
S9 250 250 646 1,195 1,876 9,534 9,534
S10 255 255 613 1,226 2,396 7,433 7,433
S11 253 253 1,349 1,683 2,453 9,811 9,811
S12 253 253 1,005 1,697 2,578 9,484 9,484
S13 267 267 1,216 1,625 2,133 9,321 9,321
S14 251 251 735 1,409 2,423 9,998 9,998
S15 250 250 1,352 1,631 2,069 8,908 8,908
S16 251 251 1,414 1,696 2,114 9,597 9,597
S17 269 269 1,135 1,366 1,696 8,687 8,687
S18 274 274 1,229 1,487 1,850 8,398 8,398
S19 263 263 1,049 1,363 1,671 8,625 8,625
S20 250 250 650 1,202 1,978 7,130 7,130
S21 252 252 795 1,240 1,914 9,417 9,417
S22 251 251 684 1,188 2,118 7,458 7,458
S23 254 254 833 1,045 1,662 5,039 5,039
S24 251 251 527 730 1,476 5,346 5,346
S25 251 251 805 1,081 1,769 9,126 9,126
S26 252 252 996 1,241 2,150 6,510 6,510
S27 252 252 786 1,591 2,603 8,325 8,325
S28 251 251 1,261 1,574 2,430 8,805 8,805
S29 251 251 1,204 1,518 2,726 9,877 9,877
S30 250 250 1,069 1,666 2,855 8,856 8,856
S31 253 253 1,312 2,050 3,263 6,680 6,680
S32 260 260 1,064 1,750 2,704 7,821 7,821
S33 256 256 870 1,705 2,771 8,893 8,893
S34 250 250 1,121 1,724 2,828 11,797 11,797
S35 250 250 706 1,649 2,666 10,391 10,391
S36 255 255 916 1,631 2,332 10,529 10,529

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 0.21 0.57 2.12 14.95 14.95
S2 0.00 0.00 2.16 4.19 8.95 14.98 14.98
S3 0.00 0.00 0.85 1.72 2.92 14.92 14.92
S4 0.00 0.00 2.93 4.49 7.30 15.00 15.00
S5 0.00 0.00 1.72 3.21 4.35 14.56 14.56
S6 0.00 0.00 1.35 2.76 5.62 14.95 14.95
S7 0.00 0.00 1.21 2.45 4.41 14.82 14.82
S8 0.00 0.00 1.82 3.54 6.39 14.99 14.99
S9 0.00 0.00 1.11 2.20 3.77 14.81 14.81
S10 0.00 0.00 1.45 3.19 6.02 15.00 15.00
S11 0.00 0.00 3.27 5.56 7.76 14.96 14.96
S12 0.00 0.00 1.98 4.71 7.69 14.97 14.97
S13 0.00 0.00 3.09 4.82 6.72 15.00 15.00
S14 0.00 0.00 1.84 3.94 6.47 14.86 14.86
S15 0.00 0.00 3.16 4.19 5.40 14.93 14.93
S16 0.00 0.00 2.70 3.62 4.70 14.38 14.38
S17 0.00 0.00 2.96 3.91 5.13 14.86 14.86
S18 0.00 0.00 2.44 3.32 4.55 13.61 13.61
S19 0.72 0.72 4.30 5.25 6.87 14.64 14.64
S20 0.08 0.08 0.43 1.01 2.66 13.67 13.67
S21 0.00 0.00 0.91 2.31 3.68 14.75 14.75
S22 0.00 0.00 1.27 3.00 5.20 14.82 14.82
S23 0.00 0.00 2.15 3.28 4.41 14.96 14.96
S24 0.00 0.00 1.67 2.48 3.33 12.74 12.74
S25 0.00 0.00 0.18 0.86 2.63 14.96 14.96
S26 0.00 0.00 1.58 2.59 4.08 14.93 14.93
S27 0.00 0.00 1.21 3.11 5.06 14.90 14.90
S28 0.00 0.00 3.43 4.90 6.46 14.76 14.76
S29 0.09 0.09 3.51 5.09 6.84 14.97 14.97
S30 0.00 0.00 1.43 2.73 4.12 14.75 14.75
S31 0.00 0.00 1.36 3.12 5.39 14.96 14.96
S32 0.00 0.00 2.40 4.30 6.82 14.43 14.43
S33 0.00 0.00 1.25 3.01 5.71 14.99 14.99
S34 0.00 0.00 4.04 6.11 8.33 14.97 14.97
S35 0.08 0.08 1.67 5.54 8.65 14.95 14.95
S36 0.00 0.00 1.33 4.31 6.72 14.95 14.95


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.

S1 S2 S3 S4 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 S21 S22 S23 S24 S25 S26 S27 S28 S29 S30 S31 S32 S33 S34 S35 S36
S1 2454 1 1 4 0 0 0 1 0 0 0 0 0 0 0 0 0 3 4 4 8 4 1 5 2 1 0 0 1 0 0 0 1 0 0
S2 1 739 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 3 0 0 0 5 1 0 0 0 0 0 0 0 0 0 0
S3 1 0 303 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 3 1 0 2 1 0 0 0 0 0 0 0 0 0 0
S4 4 6 0 1383 0 0 0 0 1 1 0 0 0 0 0 0 0 2 2 1 1 4 2 6 1 0 0 0 0 0 0 0 0 0 0
S6 0 0 0 0 549 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0
S7 0 0 0 0 0 586 276 159 265 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 1 0 0
S8 0 0 0 0 0 276 2628 216 424 3 0 1 0 1 4 1 0 0 0 0 0 0 0 0 0 2 20 0 0 0 1 1 1 0 1
S9 1 0 1 0 0 159 216 2289 199 2 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 3 17 0 2 0 0 4 1 0 2
S10 0 0 0 1 0 265 424 199 1406 0 2 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 24 0 1 0 0 3 0 0 0
S11 0 0 0 1 0 0 3 2 0 2660 21 0 0 0 3 1 0 0 0 0 0 0 0 0 0 0 0 1 1 2 0 1 3 0 0
S12 0 0 0 0 0 0 0 0 2 21 1939 0 2 2 0 1 0 0 0 0 0 0 0 0 0 2 0 1 2 2 1 0 2 0 0
S13 0 0 0 0 0 0 1 2 0 0 0 653 63 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1
S14 0 0 0 0 0 0 0 2 0 0 2 63 660 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 2 0 0 1
S15 0 0 0 0 1 0 1 1 0 0 2 0 0 1578 2 2 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 2 0 0
S16 0 0 0 0 0 1 4 0 2 3 0 0 0 2 1967 0 0 0 0 0 0 0 0 2 0 2 1 0 3 0 0 0 4 1 0
S17 0 0 0 0 0 0 1 0 1 1 1 1 0 2 0 1524 26 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0
S18 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 26 1013 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1
S19 3 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 735 3 3 2 2 1 0 2 0 0 0 0 0 0 0 0 0 0
S20 4 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 3 902 0 0 2 0 3 1 0 0 0 0 0 0 0 0 0 0
S21 4 3 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1256 2 2 3 8 4 0 0 0 0 0 0 0 0 0 0
S22 8 0 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 1626 5 1 3 4 0 0 0 0 0 0 0 0 0 1
S23 4 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 5 1991 3 4 1 0 0 0 0 0 0 1 1 0 0
S24 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 3 1 3 672 1 3 0 0 0 0 0 0 0 1 0 0
S25 5 5 2 6 0 0 0 0 0 0 0 0 0 0 2 1 0 0 3 8 3 4 1 2749 5 0 0 0 0 0 0 0 0 0 0
S26 2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 2 1 4 4 1 3 5 1773 0 0 0 0 0 0 0 0 0 0
S27 1 0 0 0 1 0 2 3 0 0 2 0 0 1 2 1 0 0 0 0 0 0 0 0 0 1533 1 0 1 0 0 2 1 0 0
S28 0 0 0 0 0 12 20 17 24 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 1 884 0 0 0 0 1 0 0 0
S29 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1282 1 0 1 1 0 0 1
S30 1 0 0 0 1 0 0 2 1 1 2 1 0 0 3 0 1 0 0 0 0 0 0 0 0 1 0 1 1808 0 0 0 2 2 0
S31 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 906 0 1 1 0 0
S32 0 0 0 0 0 0 1 0 0 0 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 729 0 1 0 0
S33 0 0 0 0 0 0 1 4 3 1 0 0 2 1 0 0 0 0 0 0 0 1 0 0 0 2 1 1 0 1 0 2571 3 0 0
S34 1 0 0 0 0 1 1 1 0 3 2 0 0 2 4 0 0 0 0 0 0 1 1 0 0 1 0 0 2 1 1 3 2733 1 3
S35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 1117 0
S36 0 0 0 0 0 0 1 2 0 0 0 1 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 3 0 1410

3.3.2 Jaccard Index

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

S1 S2 S3 S4 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 S21 S22 S23 S24 S25 S26 S27 S28 S29 S30 S31 S32 S33 S34 S35 S36
S1 100.00 0.06 0.07 0.21 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.19 0.24 0.22 0.39 0.18 0.06 0.19 0.09 0.05 0.00 0e+00 0.05 0.00 0.00 0.00 0.04 0.00 0.00
S2 0.06 100.00 0.00 0.57 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.30 0.00 0.00 0.00 0.29 0.08 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S3 0.07 0.00 100.00 0.00 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.19 0.00 0.00 0.31 0.09 0.00 0.13 0.10 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S4 0.21 0.57 0.00 100.00 0.00 0.00 0.00 0.00 0.07 0.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.19 0.18 0.08 0.07 0.24 0.19 0.29 0.06 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S6 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.09 0.00 0.00 0.13 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.00 0e+00 0.08 0.00 0.00 0.00 0.00 0.00 0.00
S7 0.00 0.00 0.00 0.00 0.00 100.00 17.17 11.06 26.61 0.00 0.00 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.63 0e+00 0.00 0.00 0.00 0.00 0.06 0.00 0.00
S8 0.00 0.00 0.00 0.00 0.00 17.17 100.00 8.79 21.02 0.11 0.00 0.06 0.00 0.05 0.17 0.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 1.14 0e+00 0.00 0.00 0.06 0.04 0.04 0.00 0.05
S9 0.04 0.00 0.08 0.00 0.00 11.06 8.79 100.00 10.77 0.08 0.00 0.14 0.14 0.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.16 1.07 0e+00 0.10 0.00 0.00 0.16 0.04 0.00 0.11
S10 0.00 0.00 0.00 0.07 0.00 26.61 21.02 10.77 100.00 0.00 0.12 0.00 0.00 0.00 0.12 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.10 0e+00 0.06 0.00 0.00 0.15 0.00 0.00 0.00
S11 0.00 0.00 0.00 0.05 0.00 0.00 0.11 0.08 0.00 100.00 0.91 0.00 0.00 0.00 0.13 0.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 5e-02 0.04 0.11 0.00 0.04 0.11 0.00 0.00
S12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.12 0.91 100.00 0.00 0.15 0.11 0.00 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.12 0.00 6e-02 0.11 0.14 0.07 0.00 0.09 0.00 0.00
S13 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.14 0.00 0.00 0.00 100.00 9.60 0.00 0.00 0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1e-01 0.08 0.00 0.00 0.00 0.00 0.00 0.10
S14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.00 0.15 9.60 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.13 0e+00 0.00 0.00 0.29 0.12 0.00 0.00 0.10
S15 0.00 0.00 0.00 0.00 0.09 0.00 0.05 0.05 0.00 0.00 0.11 0.00 0.00 100.00 0.11 0.13 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.00 0e+00 0.00 0.00 0.09 0.05 0.09 0.00 0.00
S16 0.00 0.00 0.00 0.00 0.00 0.08 0.17 0.00 0.12 0.13 0.00 0.00 0.00 0.11 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.08 0.00 0.11 0.07 0e+00 0.16 0.00 0.00 0.00 0.17 0.06 0.00
S17 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.00 0.07 0.05 0.06 0.09 0.00 0.13 0.00 100.00 2.05 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.06 0.07 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S18 0.00 0.00 0.00 0.00 0.13 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.08 0.00 2.05 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.11 0e+00 0.07 0.00 0.00 0.00 0.00 0.00 0.08
S19 0.19 0.14 0.19 0.19 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.37 0.30 0.17 0.15 0.14 0.00 0.16 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S20 0.24 0.00 0.00 0.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.37 100.00 0.00 0.00 0.14 0.00 0.16 0.07 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S21 0.22 0.30 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.30 0.00 100.00 0.14 0.12 0.31 0.40 0.26 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S22 0.39 0.00 0.31 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.17 0.00 0.14 100.00 0.28 0.09 0.14 0.24 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.07
S23 0.18 0.00 0.09 0.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.15 0.14 0.12 0.28 100.00 0.23 0.17 0.05 0.00 0.00 0e+00 0.00 0.00 0.00 0.04 0.04 0.00 0.00
S24 0.06 0.00 0.00 0.19 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.31 0.09 0.23 100.00 0.06 0.25 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.06 0.00 0.00
S25 0.19 0.29 0.13 0.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.08 0.05 0.00 0.00 0.16 0.40 0.14 0.17 0.06 100.00 0.22 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S26 0.09 0.08 0.10 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.00 0.16 0.07 0.26 0.24 0.05 0.25 0.22 100.00 0.00 0.00 0e+00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S27 0.05 0.00 0.00 0.00 0.10 0.00 0.10 0.16 0.00 0.00 0.12 0.00 0.00 0.06 0.11 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.08 0e+00 0.06 0.00 0.00 0.10 0.05 0.00 0.00
S28 0.00 0.00 0.00 0.00 0.00 1.63 1.14 1.07 2.10 0.00 0.00 0.00 0.13 0.00 0.07 0.00 0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.08 100.00 0e+00 0.00 0.00 0.00 0.06 0.00 0.00 0.00
S29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.06 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1e+02 0.06 0.00 0.10 0.05 0.00 0.00 0.07
S30 0.05 0.00 0.00 0.00 0.08 0.00 0.00 0.10 0.06 0.04 0.11 0.08 0.00 0.00 0.16 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.00 6e-02 100.00 0.00 0.00 0.00 0.09 0.14 0.00
S31 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.11 0.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0e+00 0.00 100.00 0.00 0.06 0.05 0.00 0.00
S32 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.07 0.00 0.29 0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1e-01 0.00 0.00 100.00 0.00 0.06 0.00 0.00
S33 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.16 0.15 0.04 0.00 0.00 0.12 0.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.10 0.06 5e-02 0.00 0.06 0.00 100.00 0.11 0.00 0.00
S34 0.04 0.00 0.00 0.00 0.00 0.06 0.04 0.04 0.00 0.11 0.09 0.00 0.00 0.09 0.17 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.06 0.00 0.00 0.05 0.00 0e+00 0.09 0.05 0.06 0.11 100.00 0.05 0.14
S35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0e+00 0.14 0.00 0.00 0.00 0.05 100.00 0.00
S36 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.11 0.00 0.00 0.00 0.10 0.10 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 7e-02 0.00 0.00 0.00 0.00 0.14 0.00 100.00


3.4 Doublet Cell Detection using Scrublet Scoring System

Observed scores are used for doublet classification. Dashed line indicates the threshold used to identify doublets.

3.4.1 Observed scores

3.4.2 Simulated scores


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

3.5.1 Number of cells and genes per sample

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

3.5.2 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.


3.6 Key QC Metrics of Merged Samples

min 0% 25% 50% 75% 100% max
UMI per cell 500 500 2,350 4,341 10,520 248,954 248,954
Gene per cell 250 250 863 1,438 2,232 11,797 11,797
Mitochondrial (%) per cell 0.00 0.00 1.54 3.37 5.64 15.00 15.00

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

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

3.7.1 Signacx SPRING Projection

3.7.2 Seurat UMAP Projection

3.7.3 Seurat UMAP Projection (no-batch correction)


3.8 Visualizing Cell QC Metrics Using Dimensionality Reduction

Note: QC metrics based on kernel density estimation.

3.8.1 UMI per cell - SPRING Projection

3.8.2 Gene per cell - SPRING Projection

3.8.3 Mitochondrial (%) per cell - SPRING Projection

3.8.4 UMI per cell - UMAP Projection

3.8.5 Gene per cell - UMAP Projection

3.8.6 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


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] spatstat.utils_3.0-4    rmarkdown_2.25         
## [101] RhpcBLASctl_0.23-42     XVector_0.42.0         
## [103] htmltools_0.5.7         pkgconfig_2.0.3        
## [105] highr_0.10              fastmap_1.1.1          
## [107] rlang_1.1.2             GlobalOptions_0.1.2    
## [109] htmlwidgets_1.6.4       shiny_1.8.0            
## [111] jquerylib_0.1.4         farver_2.1.1           
## [113] zoo_1.8-12              jsonlite_1.8.8         
## [115] mclust_6.0.1            R.oo_1.25.0            
## [117] RCurl_1.98-1.13         magrittr_2.0.3         
## [119] GenomeInfoDbData_1.2.11 dotCall64_1.1-1        
## [121] munsell_0.5.0           stringi_1.8.2          
## [123] rootSolve_1.8.2.4       zlibbioc_1.48.0        
## [125] MASS_7.3-60             plyr_1.8.9             
## [127] parallel_4.3.2          listenv_0.9.0          
## [129] lmom_3.0                deldir_2.0-2           
## [131] splines_4.3.2           tensor_1.5             
## [133] circlize_0.4.15         locfit_1.5-9.8         
## [135] spatstat.geom_3.2-7     markdown_1.12          
## [137] RcppHNSW_0.5.0          reshape2_1.4.4         
## [139] evaluate_0.23           foreach_1.5.2          
## [141] httpuv_1.6.13           RANN_2.6.1             
## [143] tidyr_1.3.0             getopt_1.20.4          
## [145] polyclip_1.10-6         future_1.33.0          
## [147] clue_0.3-65             scattermore_1.2        
## [149] xtable_1.8-4            e1071_1.7-14           
## [151] RSpectra_0.16-1         later_1.3.2            
## [153] viridisLite_0.4.2       class_7.3-22           
## [155] tibble_3.2.1            cluster_2.1.6          
## [157] globals_0.16.2