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2k Brain Cells from an E18 Mouse

Cells from a combined cortex, hippocampus and sub ventricular zone of an E18 mouse.

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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
2440 60250 1636 147010995 97.0 81.7 97.8 97.7 87.5 81.1 2.8 17.4 61.0 57.3 2.1 74.9 17200 3465

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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 Gpm6a 3.70233432359549e-129 1.40173762228014 0.909 0.458 1.14968587750611e-124
0 Neurod6 9.53419064954915e-113 1.10385557725469 0.993 0.578 2.9606522224045e-108
0 Cd24a 1.91778615213668e-110 0.962138427126802 0.987 0.735 5.95530133823003e-106
0 Gria2 1.40926899950229e-108 0.839708070730201 0.975 0.504 4.37620302415445e-104
0 Syt4 2.12204214906877e-106 1.23316694820313 0.626 0.171 6.58957748550326e-102
0 Neurod2 1.38798608422995e-105 0.864921589863384 0.932 0.418 4.31011318735926e-101
0 Ntm 1.38571195484114e-103 1.02108953565514 0.552 0.122 4.30305133336819e-99
0 Bhlhe22 2.32261801049248e-102 1.01029154552787 0.607 0.155 7.21242570798229e-98
0 Nrp1 4.13366537085338e-101 1.05447194690652 0.745 0.252 1.2836271076111e-96
0 Dok5 1.04438521163311e-99 1.06996703662068 0.628 0.187 3.24312939768428e-95
1 Hnrnpf 2.7915960341024e-42 -0.648053491432223 0.181 0.613 8.66874316469817e-38
1 Cnbp 6.07434327808589e-41 -0.671126802193924 0.286 0.735 1.88626581814401e-36
1 Anp32e 5.55606110454063e-40 -0.674984717894403 0.128 0.514 1.725323654793e-35
1 Selenof 1.87988879077434e-38 -0.533514927465391 0.202 0.633 5.83761866199156e-34
1 Pgk1 1.03583589528772e-37 -0.653147157803657 0.128 0.506 3.21658120563696e-33
1 Actr3 1.01824323035257e-34 -0.494633343128376 0.155 0.55 3.16195070321383e-30
1 Eif3e 1.60191404774921e-34 -0.522772718062279 0.29 0.73 4.97442369247561e-30
1 Ppp1cc 4.64301994382659e-33 -0.478381241867074 0.229 0.646 1.44179698315647e-28
1 Bzw1 3.6978602717778e-32 -0.369640521272457 0.218 0.627 1.14829655019516e-27
1 Sae1 3.87284167745343e-32 -0.555162819886792 0.097 0.42 1.20263352609961e-27
2 Eomes 2.30454053687184e-110 1.55734112681905 0.5 0.072 7.15628972914812e-106
2 Rnd2 1.1214571995406e-86 1.1183956236643 0.59 0.14 3.48246104173344e-82
2 Mfap4 3.8462352769696e-85 1.29847405509398 0.581 0.143 1.19437144055737e-80
2 Pcp4 2.03132524188572e-78 1.60119316990291 0.694 0.244 6.30787427362772e-74
2 Nrn1 1.74392441584195e-77 0.997278411138661 0.455 0.088 5.415408488514e-73
2 Ezr 4.9134730133849e-77 1.13078551197212 0.66 0.21 1.52578077484641e-72
2 Mdk 6.04090509602223e-74 1.25780123677662 0.89 0.497 1.87588225946778e-69
2 Neurog2 6.09946837522891e-65 1.44741908829025 0.486 0.129 1.89406791455983e-60
2 Elavl4 1.45409462826174e-63 1.0558786014803 0.663 0.233 4.51540004914119e-59
2 Lhx2 5.11218729667267e-63 1.04046706223413 0.817 0.386 1.58748752123577e-58
3 Dlx2 1.23045863271837e-202 2.47068471193736 0.632 0.047 3.82094319218035e-198
3 Dlx6os1 6.78819828876106e-188 2.33485651195504 0.581 0.04 2.10793921460897e-183
3 Sp9 1.10658652758916e-175 2.29225696333613 0.533 0.033 3.43628314412263e-171
3 Dlx1 1.21625790665518e-162 2.27683836360532 0.556 0.048 3.77684567753632e-158
3 Nrxn3 5.03935396492669e-157 2.15546571053283 0.549 0.051 1.56487058672868e-152
3 Dlx5 2.39994021597285e-148 1.73965617550848 0.422 0.02 7.45253435266049e-144
3 Gad2 9.05197001265088e-121 1.7684280900452 0.46 0.048 2.81090824802848e-116
3 Gad1 1.74097974152574e-118 1.59627110459491 0.359 0.02 5.40626439135989e-114
3 Meg3 5.73331903789237e-94 2.28533947390393 0.838 0.408 1.78036756083672e-89
3 Arx 6.06158582603443e-70 1.72615076337594 0.448 0.1 1.88230424655847e-65
4 Pbk 3.239304666022e-211 2.46807845808438 0.773 0.067 1.00590127793981e-206
4 Ccna2 5.29025381611371e-206 1.79350501538892 0.62 0.03 1.64278251751779e-201
4 Cdk1 3.22278026157649e-185 2.06787975749699 0.638 0.044 1.00076995462735e-180
4 Nusap1 6.33855029840532e-183 1.96690600325159 0.585 0.033 1.9683100241638e-178
4 Top2a 7.25960857028151e-176 2.3803472947021 0.712 0.072 2.25432624932952e-171
4 Birc5 3.94399632471634e-175 2.14781649168446 0.738 0.079 1.22472917871416e-170
4 Tpx2 1.25246540746125e-174 1.77509425115384 0.611 0.042 3.88928082978942e-170
4 Spc25 9.60073598402142e-173 1.93846652867495 0.642 0.052 2.98131654511817e-168
4 Mis18bp1 4.7843698214389e-164 1.10232072112213 0.45 0.015 1.48569036065142e-159
4 Rrm2 2.29962389293113e-161 2.47741437513768 0.755 0.102 7.14102207471903e-157
5 Alas2 5.07501950408699e-157 3.83021019109992 0.765 0.081 1.57594580660413e-152
5 Ube2l6 6.56174619876841e-124 2.44424836423575 0.604 0.057 2.03761904710355e-119
5 Tmsb4x 8.69146915522627e-92 -4.14357417564703 0.658 0.996 2.69896191677241e-87
5 Ptma 6.71377526987792e-91 -4.37062232135008 0.463 0.993 2.08482863455519e-86
5 Stmn1 7.7186472714139e-90 -3.32311110815603 0.738 0.995 2.39687153719216e-85
5 Tmsb10 2.03292230648736e-89 -4.37797891816921 0.49 0.991 6.31283363833519e-85
5 Tuba1a 2.47945582621553e-89 -3.68952645955269 0.718 0.995 7.69945417714708e-85
5 H3f3b 6.5273134366716e-89 -4.22679528627836 0.443 0.985 2.02692664148963e-84
5 Rps19 1.86253876705257e-87 -3.16627056276466 0.564 0.983 5.78374163332835e-83
5 Malat1 9.48714232261219e-87 -5.8830296983911 0.658 0.981 2.94604230544076e-82
6 Phgdh 4.08482446471106e-108 2.47492715015039 0.818 0.137 1.26846054102672e-103
6 Aldoc 4.10145828634183e-92 2.99932649526974 0.765 0.143 1.27362584165773e-87
6 Mt2 5.67614395043733e-90 2.80773455040219 0.689 0.108 1.7626129809293e-85
6 Ccdc80 5.33045343534122e-81 1.3167011194812 0.371 0.025 1.65526570527651e-76
6 Tnc 8.34468526626188e-80 2.11935632515707 0.47 0.047 2.5912751157323e-75
6 Ttyh1 2.45928816962351e-78 1.54166452345151 0.492 0.054 7.6368275531319e-74
6 Vim 1.16950428810311e-75 2.70611827703373 0.871 0.266 3.63166166584658e-71
6 Mt3 5.50745780275845e-75 3.45548950803232 0.879 0.302 1.71023087149058e-70
6 Mt1 1.22332228249525e-73 2.48288500901836 0.795 0.192 3.79878268383251e-69
6 Rgcc 4.87522003691583e-72 1.61477899041497 0.462 0.052 1.51390207806347e-67
7 Mndal 9.88712214953262e-103 0.895288732080387 0.379 0.013 3.07024804109437e-98
7 Kcnk1 4.19678307683913e-101 1.04789842348303 0.463 0.023 1.30322704885085e-96
7 Fam163a 3.90286644966562e-90 0.568777254711227 0.263 0.005 1.21195711861467e-85
7 Rerg 6.83810989651995e-81 0.548520872215948 0.274 0.008 2.12343826616634e-76
7 Crym 2.41593391373922e-69 1.63076729542246 0.505 0.049 7.50219958233439e-65
7 Nhlh2 3.62599575239747e-69 1.38575124415601 0.421 0.032 1.12598046099199e-64
7 Lhx9 1.41483048949731e-67 0.774634269709811 0.347 0.02 4.39347311903599e-63
7 Calb2 1.61526066360201e-66 2.05141973940719 0.6 0.077 5.01586893868332e-62
7 Snca 3.99849656917862e-62 2.08306060050762 0.758 0.139 1.24165313962704e-57
7 Zfp385b 7.21619326365747e-62 0.585782800774188 0.295 0.015 2.24084449416356e-57
8 BC028528 1.1319960713389e-180 2.08591634499504 0.509 0.005 3.51518740032867e-176
8 Foxq1 2.41961904605577e-154 2.07260231970578 0.434 0.005 7.51364302371698e-150
8 Arhgdib 5.67529972928628e-154 2.21354950294303 0.528 0.009 1.76235082493527e-149
8 Selenop 7.0599237021183e-152 3.64594637833835 0.717 0.024 2.19231810721879e-147
8 Cd34 2.76904136670888e-149 1.95481644632211 0.358 0.002 8.5987041560411e-145
8 Tgfb1 3.88502508549952e-145 1.50633914168498 0.396 0.004 1.20641683980017e-140
8 Grap 2.67514281914396e-144 1.55081125557215 0.415 0.005 8.30712099628773e-140
8 Slc40a1 1.01540028366931e-140 1.9964784990003 0.415 0.005 3.15312250087832e-136
8 Flt1 1.47066719223508e-132 2.35409082943033 0.396 0.005 4.56686283204759e-128
8 Tm6sf1 1.98677311450192e-131 1.09582977665112 0.377 0.004 6.1695265524628e-127
9 Rcan2 1.07366721687448e-137 4.79965240317891 0.9 0.029 3.33405880856032e-133
9 Slc38a7 4.18935174421533e-122 4.9383227928969 0.933 0.038 1.30091939713119e-117
9 Mid1 3.28359261287511e-108 5.3806272196175 1 0.053 1.01965401407611e-103
9 Gm16499.1 3.865182337641e-107 2.17844499530256 0.367 0.004 1.20025507130766e-102
9 Gm16001 1.15942895823163e-89 2.00505504212763 0.3 0.003 3.6003747439967e-85
9 U2af1l4 1.30275990235758e-85 5.49152517324286 0.967 0.066 4.04546032479098e-81
9 Stxbp3 2.270570204026e-70 3.13433805495137 0.567 0.023 7.05080165456195e-66
9 Ptprb 5.85981593676647e-68 1.83929339841273 0.333 0.007 1.81964864284409e-63
9 Dusp4 1.28693388841831e-65 5.36107017198404 1 0.102 3.99631580370538e-61
9 Bcas3 9.92089924711806e-59 5.35455956608887 0.833 0.074 3.08073684320757e-54



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.