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8k PBMCs from a Healthy Donor

Peripheral blood mononuclear cells (PBMCs) from a healthy donor (same donor as pbmc4k). PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell).

CellRanger Metadata

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Accession Estimated No. of Cells Mean Reads per Cell Median Genes per Cell No. of Reads % Valid Barcodes % sequencing Saturation % Q30 Bases in Barcode % Q30 Bases in UMI % Reads Mapped to Genome % Reads Mapped Confidently to Genome % Reads Mapped Confidently to Intergenic Regions % Reads Mapped Confidently to Intronic Regions % Reads Mapped Confidently to Exonic Regions % Reads Mapped Confidently to Transcriptome % Reads Mapped Antisense to Gene % Fraction Reads in Cells Total Genes Detected Median UMI Counts Per Cell
8708 90040 1246 784064148 98.5 90.8 98.2 98.2 95.5 93.3 3.4 24.3 65.6 61.9 1.1 93.7 21189 3905

CellxGene data viewer







Top 10 Marker Genes per Cluster

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Accession Seurat Cluster Gene Symbol P Value Average Log Pct 1 Pct 2 Adjusted P Value
0 CCR7 0 1.38842950645581 0.679 0.157 0
0 LEF1 0 1.37617656273172 0.681 0.161 0
0 LDHB 0 1.14581082845546 0.967 0.615 0
0 TRAC 0 1.03135948506602 0.959 0.479 0
0 CLIC1 0 -1.45655276348993 0.298 0.727 0
0 HLA-DQB1 0 -2.70721989183554 0.105 0.61 0
0 HLA-DPB1 0 -2.71400013954059 0.25 0.668 0
0 HLA-DPA1 0 -2.79175877681996 0.186 0.636 0
0 HLA-DRB1 0 -3.33317890164281 0.198 0.685 0
0 HLA-DRA 0 -3.70045664882997 0.365 0.726 0
1 S100A9 0 3.28951409004238 0.999 0.509 0
1 LYZ 0 3.17418430766095 0.999 0.503 0
1 S100A8 0 3.00014927201872 0.998 0.441 0
1 FCN1 0 2.76851361063475 0.995 0.196 0
1 S100A12 0 2.75441506304847 0.913 0.131 0
1 AC020656.1 0 2.63438477556619 0.979 0.165 0
1 TYROBP 0 2.61890616722897 0.999 0.332 0
1 LGALS2 0 2.59023821155411 0.924 0.137 0
1 MNDA 0 2.49006167092784 0.985 0.177 0
1 CSTA 0 2.46214996761802 0.97 0.146 0
2 IL32 0 1.41572263425042 0.979 0.532 0
2 IL7R 1.75255530939672e-249 1.34799298603117 0.8 0.345 5.87771999665471e-245
2 TRAC 8.24485133120877e-247 1.16663126540364 0.969 0.527 2.7651582394608e-242
2 LTB 1.34035799576099e-246 1.23127779923952 0.981 0.721 4.49529264618322e-242
2 AQP3 1.34780801163883e-219 0.984411400479276 0.477 0.117 4.52027850943432e-215
2 ITGB1 1.534646784729e-210 1.25723779683449 0.614 0.228 5.14689838662413e-206
2 LDHB 1.12458534140538e-201 0.926291120022681 0.944 0.654 3.77163431800537e-197
2 CD3D 3.95778856103725e-177 0.872309772553389 0.938 0.501 1.32736312760067e-172
2 CD40LG 3.90977299438147e-171 0.729459256163772 0.343 0.071 1.31125966685566e-166
2 HLA-DRA 1.05976300429762e-168 -3.4128391448049 0.419 0.681 3.55423316381337e-164
3 IGHM 0 4.97639889464851 0.954 0.185 0
3 IGKC 0 4.57127759266603 0.789 0.221 0
3 IGLC2 0 4.06286696436225 0.408 0.034 0
3 CD79A 0 3.82011648855142 0.984 0.082 0
3 IGLC3 0 3.76316041160018 0.363 0.028 0
3 CD79B 0 3.49990071232102 0.98 0.153 0
3 IGHD 0 3.43453617894678 0.867 0.036 0
3 MS4A1 0 3.34793072273766 0.948 0.06 0
3 TCL1A 0 3.345328877973 0.666 0.043 0
3 LINC00926 0 2.34040740476792 0.699 0.023 0
4 CCL5 0 3.4213032233125 0.989 0.204 0
4 GZMK 0 2.80731316020721 0.706 0.073 0
4 NKG7 0 2.64532473643354 0.966 0.205 0
4 CST7 0 2.32058201807753 0.865 0.101 0
4 TRGC2 0 2.31606144791052 0.662 0.064 0
4 GZMA 0 2.30509311546871 0.896 0.13 0
4 CMC1 0 2.19449536656108 0.595 0.13 0
4 LYAR 0 1.93306991247497 0.787 0.17 0
4 CTSW 0 1.89129118986023 0.915 0.249 0
4 IL32 0 1.81150750470093 0.986 0.544 0
5 S100A12 0 2.44421147041528 0.905 0.209 0
5 AC020656.1 1.93695475342028e-293 2.2920463281294 0.928 0.25 6.49615885202093e-289
5 S100A8 1.80321640544509e-257 2.85814999017204 0.983 0.498 6.04762718058176e-253
5 MNDA 1.39818418241412e-255 2.017103589638 0.919 0.263 4.68923011098046e-251
5 VCAN 7.94794788391904e-236 1.9551018898653 0.783 0.195 2.66558276130877e-231
5 S100A9 2.44156727305347e-231 2.42501850786629 0.987 0.559 8.18852832036674e-227
5 FCN1 2.47950019198282e-225 1.77053761127274 0.921 0.28 8.31574774387197e-221
5 CSTA 2.28456273424184e-204 1.67997627063767 0.83 0.238 7.66196649810028e-200
5 TYROBP 4.17518137989887e-204 1.75234178024542 0.981 0.4 1.40027233119048e-199
5 LST1 4.14268553942383e-203 1.66143093606876 0.951 0.364 1.38937387621196e-198
6 FOS 6.154784439048e-123 -1.81945617201068 0.556 0.932 2.06419160516792e-118
6 DUSP1 3.46021205279954e-109 -1.57107175629429 0.472 0.912 1.16048591826791e-104
6 CYBA 2.21807141819454e-89 -1.36563864433333 0.57 0.921 7.43896792234085e-85
6 OAZ1 2.8190728828396e-87 -1.24937711870387 0.638 0.95 9.45460663446745e-83
6 H3F3A 6.79151370182763e-86 -1.18136374748109 0.631 0.953 2.27773786531895e-81
6 ZFP36 2.06066238945003e-85 -1.38063325572546 0.258 0.773 6.9110495217375e-81
6 JUN 4.03250362354615e-84 -1.41325653087746 0.404 0.865 1.35242106526491e-79
6 CD74 1.88075894298489e-77 -2.63140423408332 0.556 0.879 6.30768934298273e-73
6 JUNB 1.44082878125043e-72 -1.04543619045883 0.693 0.958 4.8322515665577e-68
6 GAPDH 9.4408425776615e-72 -1.23631981199412 0.532 0.887 3.16626978369611e-67
7 GNLY 0 4.81670383619186 0.969 0.144 0
7 PRF1 0 3.60474265925967 0.95 0.119 0
7 FGFBP2 0 3.54827612773261 0.783 0.053 0
7 KLRF1 0 3.2243614712169 0.931 0.03 0
7 SPON2 0 3.15640961151269 0.755 0.044 0
7 KLRD1 0 3.12154017145077 0.981 0.1 0
7 GZMB 0 3.10118162749636 0.818 0.054 0
7 HOPX 0 2.88961661811534 0.906 0.11 0
7 CLIC3 0 2.88515236921842 0.739 0.049 0
7 CST7 0 2.77384756174103 0.937 0.159 0
8 FCER1A 0 3.26460855673491 0.778 0.022 0
8 CLEC10A 0 1.90911399364806 0.597 0.016 0
8 GSN 0 1.22018187454845 0.753 0.062 0
8 ENHO 0 1.20220230419874 0.519 0.005 0
8 PLD4 0 1.04811293351681 0.761 0.063 0
8 CACNA2D3 0 0.818444026834952 0.609 0.036 0
8 UPK3A 0 0.652083636489995 0.523 0.027 0
8 AC004817.3 0 0.558998221148613 0.354 0.007 0
8 CLIC2 0 0.544136115709482 0.412 0.009 0
8 FLT3 0 0.46653766648951 0.317 0.006 0
9 FCGR3A 0 3.40942692072211 0.97 0.076 0
9 MS4A7 0 2.77664927529672 0.943 0.124 0
9 SMIM25 0 2.51358792256351 0.961 0.108 0
9 HES4 0 1.75536009276363 0.722 0.017 0
9 CDKN1C 0 1.66250164867149 0.696 0.005 0
9 TCF7L2 0 1.53411003371333 0.713 0.033 0
9 SIGLEC10 0 1.41998193079802 0.691 0.037 0
9 C1QA 0 1.30853673525141 0.304 0.005 0
9 MS4A4A 0 0.920508508265835 0.465 0.015 0
9 CKB 0 0.76361183871923 0.274 0.004 0
10 CD79A 1.29640269824773e-55 1.07199240447358 0.853 0.194 4.34787536938325e-51
10 RALGPS2 5.82657218820809e-52 0.643873219189806 0.569 0.095 1.95411578048123e-47
10 PAX5 1.53735615444519e-49 0.413165409697926 0.294 0.03 5.15598507077828e-45
10 ADAM28 3.81220426104442e-46 0.580017943081899 0.505 0.086 1.27853706506908e-41
10 FAM30A 5.93780106177388e-46 0.707134053897607 0.367 0.049 1.99141972009772e-41
10 CD22 2.19176146947793e-45 0.668132498636668 0.569 0.106 7.35072961633507e-41
10 MS4A1 6.5122435060602e-45 0.665870181727301 0.752 0.171 2.18407622706247e-40
10 IGHD 8.94557817708987e-45 0.982827476244372 0.651 0.14 3.0001680090324e-40
10 BCL11A 1.41610901140532e-42 0.590828396951423 0.615 0.127 4.74934640245117e-38
10 CD79B 3.92154047206626e-40 0.946697274671938 0.835 0.256 1.31520624352158e-35
11 PPBP 0 6.99323053378967 0.986 0.015 0
11 PF4 0 6.48907865336065 0.915 0.009 0
11 GNG11 0 5.80142540265276 0.972 0.016 0
11 CAVIN2 0 5.55568651654243 0.972 0.011 0
11 TUBB1 0 5.29902570599482 0.915 0.006 0
11 CLU 0 4.6137038375901 0.831 0.013 0
11 ACRBP 0 4.54901142929296 0.746 0.012 0
11 GP9 0 4.30298718103615 0.817 0.003 0
11 SPARC 0 3.98156679010145 0.817 0.005 0
11 PTCRA 0 3.62655818917512 0.592 0.01 0
12 LILRA4 0 4.14816529578482 1 0.014 0
12 SERPINF1 0 2.96178913229353 0.942 0.016 0
12 DERL3 0 2.77188895824606 0.957 0.018 0
12 LRRC26 0 2.69801749062105 0.971 0.001 0
12 SCT 0 2.69463486778418 0.855 0.001 0
12 IL3RA 0 2.51301905958358 0.942 0.009 0
12 TPM2 0 2.49950981798992 0.725 0.007 0
12 DNASE1L3 0 2.27403947247288 0.942 0.015 0
12 CLEC4C 0 2.21680955979742 0.913 0.003 0
12 LINC00996 0 1.99893207530085 0.768 0.008 0



SkewC Quality Control Output Plots


Gene Body Coverage

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Gene Body Coverage of All Cells.

Typical Coverage
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Gene Body Coverage of Typical Cells.
Skewed Coverage
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Gene Body Coverage of Skewed Cells.

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Cell Clustering Result.
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Mean Gene Body Coverage.