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2k Brain Nuclei from an Adult Mouse (>8 weeks)

Nuclei from a combined cortex, hippocampus and sub ventricular zone of an adult mouse (>8 weeks).

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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
2602 45635 714 118742315 97.3 83.9 98.3 98.1 81.1 79.3 5.7 46.4 27.2 24.2 2.0 72.4 17736 1034

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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 Brinp3 1.28620649333864e-122 1.98040376063359 0.642 0.154 3.99405702376449e-118
0 R3hdm1 1.95003976407627e-96 1.3445891130596 0.919 0.503 6.05545847938606e-92
0 Mef2c 2.52195613324325e-80 1.15338688153936 0.811 0.342 7.83143038056025e-76
0 Snhg11 3.81541271232059e-74 0.797139205779997 1 0.747 1.18480010955691e-69
0 Ptprd 1.74611257133616e-72 1.13258272559234 0.798 0.375 5.42220336777019e-68
0 Kalrn 1.97559303017961e-71 1.0957453899084 0.894 0.512 6.13480903661674e-67
0 A830036E02Rik 1.16238059093659e-57 1.43215397049759 0.354 0.088 3.6095404490354e-53
0 Arpp21 2.39500650221359e-54 0.873136935679797 0.835 0.439 7.43721369132386e-50
0 Cit 5.88397091034862e-50 1.018934040834 0.618 0.267 1.82714948679056e-45
0 Xist 5.91734842754727e-50 0.667840204819132 0.991 0.738 1.83751420720625e-45
1 mt-Nd3 1.48421042411557e-197 2.68795883232732 1 0.693 4.60891863000607e-193
1 Malat1 1.96679909777218e-193 -3.92508248183112 0.734 0.99 6.10750123831197e-189
1 Meg3 7.81362747949564e-176 -3.78523399871376 0.414 0.952 2.42636574120778e-171
1 Xist 1.00444720348198e-163 -3.61624659842997 0.127 0.909 3.11910990097259e-159
1 Snhg11 2.70983494614816e-157 -3.43879683209142 0.213 0.904 8.41485045827388e-153
1 mt-Nd5 8.99500296135686e-147 2.36840039900818 0.919 0.572 2.79321826959015e-142
1 Gria2 1.94468550445585e-140 -2.77140956487102 0.173 0.902 6.03883189698674e-136
1 Rsrp1 2.09503292660056e-110 -2.67519690980338 0.096 0.789 6.50570574697271e-106
1 Celf2 2.74543739129355e-109 -2.62976114778792 0.117 0.796 8.52540673118387e-105
1 R3hdm1 5.34782359566076e-103 -3.34943585833766 0.033 0.69 1.66065966116054e-98
2 Enpp2 1.10883353354445e-85 1.5250927220223 0.441 0.074 3.44326077171559e-81
2 Lingo2 8.97553751228331e-80 1.37762867990784 0.561 0.132 2.78717366368934e-75
2 Sorbs2 1.19731464449856e-79 1.35123885019873 0.797 0.303 3.71802116556137e-75
2 Fam19a1 3.56413233110326e-77 1.18907392817677 0.765 0.242 1.1067700127775e-72
2 Rasgrf2 3.55405736828989e-73 1.3833156650331 0.385 0.064 1.10364143457506e-68
2 2900055J20Rik 2.51000718832329e-61 1.1528843975166 0.762 0.317 7.7943253219003e-57
2 Lrfn5 4.37092554306383e-61 1.1460255363185 0.725 0.283 1.35730350888761e-56
2 Acp1 2.30371949313125e-55 1.08399324426913 0.786 0.346 7.15374014202048e-51
2 Mef2c 5.05701469456272e-55 0.960080149070737 0.837 0.373 1.57035477310256e-50
2 Cit 3.35202584224339e-54 1.06988828267853 0.703 0.28 1.04090458479184e-49
3 Acp1 1.52271158643382e-39 -1.76566261317438 0.078 0.465 4.72847628935294e-35
3 Rnf112 4.69814072933169e-30 -1.06920316338918 0.143 0.506 1.45891364067937e-25
3 Gm26917 1.6641320702344e-23 -0.875919034408447 0.227 0.566 5.16762931769889e-19
3 Ube3a 1.77375450537074e-21 -0.792301289906198 0.262 0.588 5.50803986552777e-17
3 Dtx3 3.21152972695319e-21 -0.922256738024314 0.097 0.367 9.97276326110775e-17
3 Pnisr 3.98458302036298e-20 -0.716777851932251 0.224 0.542 1.23733256531332e-15
3 Srsf5 7.50326952717689e-20 -0.882730337033575 0.132 0.413 2.32999028627424e-15
3 Cttnbp2 2.0636856305313e-19 -0.837115013537157 0.178 0.473 6.40836298848884e-15
3 AY036118 2.31629166002653e-19 -0.671012553230017 0.224 0.537 7.19278049188038e-15
3 Gls 1.26939058984356e-15 -0.647168270364294 0.143 0.395 3.9418385986412e-11
4 Pde4d 1.12225732315108e-74 1.99705776778171 0.432 0.079 3.48494566558106e-70
4 Garnl3 2.08406941799464e-73 1.89551672362412 0.543 0.133 6.47166076369875e-69
4 Col6a1 3.83483435788422e-73 1.94135399613347 0.457 0.086 1.19083111315379e-68
4 3110035E14Rik 1.16319490242368e-63 1.76469616220542 0.496 0.124 3.61206913049624e-59
4 Adgra1 2.1894139633832e-42 1.35970879820262 0.339 0.078 6.79878718049385e-38
4 Ccl27a 2.39110112133253e-42 1.52421543354924 0.575 0.233 7.42508631207391e-38
4 Nos1ap 5.34616335429928e-41 1.49174534498754 0.468 0.16 1.66014410641056e-36
4 Nfib 6.78086675178126e-40 1.38155723205111 0.589 0.253 2.10566255243063e-35
4 Me3 1.0602300765089e-37 1.46247810684346 0.35 0.096 3.2923324565831e-33
4 Nptx1 3.27000437598367e-32 1.25791311389351 0.5 0.204 1.01543445887421e-27
5 Zbtb20 1.42316306992068e-190 2.99132128485709 0.967 0.151 4.41934828102468e-186
5 Cpne7 1.29124840962731e-134 2.86123787671439 0.71 0.099 4.00971368641568e-130
5 Rnf182 4.51474178664491e-118 1.89303406498433 0.414 0.026 1.40196276700684e-113
5 Fam19a1 2.56635820515852e-108 2.32961719054321 0.91 0.265 7.96931213447874e-104
5 Gria1 1.10920001570729e-102 2.04052887014715 0.871 0.235 3.44439880877585e-98
5 Dock4 3.91736728207432e-92 1.97366748059136 0.852 0.252 1.21646006210254e-87
5 Pkp2 2.93513983369871e-89 1.34381828683724 0.305 0.018 9.11448972558461e-85
5 Ryr3 5.04455298341007e-88 1.73594750624126 0.481 0.061 1.56648503793833e-83
5 Cul4a 1.04876116497798e-77 1.90934501541847 0.686 0.16 3.25671804560612e-73
5 St6galnac5 3.05224418195984e-70 1.41236417377582 0.419 0.056 9.4781338582399e-66
6 Prox1 6.59732014578535e-117 2.25698506739538 0.315 0.007 2.04866582487073e-112
6 Dock10 1.7839199336453e-108 2.45806704082257 0.409 0.021 5.53960656994874e-104
6 Zbtb20 3.21403783418084e-97 2.71631308522032 0.898 0.182 9.98055168648178e-93
6 Sema5a 3.14464079098729e-73 1.9880825146995 0.299 0.017 9.76505304825284e-69
6 Cdh9 2.00076458249077e-53 2.04992337878944 0.409 0.055 6.21297425800857e-49
6 Ahcyl2 1.39272272455336e-43 2.30033818164681 0.575 0.154 4.32482187655554e-39
6 Epha7 3.85196167694682e-33 1.9623816113471 0.512 0.148 1.1961496595423e-28
6 Rfx3 1.13082434452768e-31 1.95978861097119 0.409 0.097 3.5115488370618e-27
6 Adcy1 6.9304262757732e-26 1.63838659825643 0.646 0.283 2.15210527141585e-21
6 Rogdi 2.60351152747969e-25 1.51620297925403 0.638 0.278 8.08468434628267e-21
7 Atp1a2 2.64598104875398e-185 4.70874801039178 0.722 0.037 8.21656495069572e-181
7 Gpr37l1 5.01538409363148e-175 3.7263688268486 0.454 0.008 1.55742722259538e-170
7 Slc1a3 2.89540365914832e-160 4.1676987397197 0.602 0.028 8.99109698275326e-156
7 Gja1 4.89085672092464e-158 2.9986178272376 0.38 0.005 1.51875773754873e-153
7 Plpp3 3.52961387287228e-151 3.60337568332992 0.398 0.008 1.09605099594303e-146
7 F3 4.86951844383412e-140 3.03893474960555 0.417 0.011 1.51213156236381e-135
7 Grin2c 1.9233520607963e-129 3.25928534020179 0.324 0.005 5.97258515439075e-125
7 Htra1 7.73299536064458e-124 3.43514317222827 0.417 0.015 2.40132704934096e-119
7 Cbs 1.51960938481679e-123 2.36863901798421 0.296 0.004 4.71884302267159e-119
7 Pbxip1 1.89856860979768e-112 2.3892519699824 0.287 0.005 5.89562510400475e-108
8 Ndrg2 1.62250782904809e-62 2.57528524790125 0.571 0.052 5.03837356154305e-58
8 Mt1 1.65130990908335e-49 3.12993160114081 0.73 0.125 5.12781266067653e-45
8 Rplp1 2.5413803636051e-45 2.89505371290811 0.794 0.179 7.89174844310292e-41
8 Glul 1.20401326520421e-41 2.66093134456102 0.54 0.074 3.73882239243863e-37
8 Aldoc 5.26325491590494e-38 2.52456295253211 0.492 0.066 1.63439854903596e-33
8 Cox8a 3.67605683809131e-33 3.05644634872708 0.714 0.202 1.1415259299325e-28
8 Rpl41 2.21631859441855e-31 2.51793115987259 0.841 0.324 6.88233413124793e-27
8 Mt2 1.34498739163037e-29 2.22611086893044 0.397 0.054 4.17658934722978e-25
8 Fth1 3.99870444781065e-28 2.3638109427531 0.905 0.516 1.24171769217864e-23
8 Meg3 8.52819921932591e-28 -4.41999945571659 0.413 0.881 2.64826170357727e-23
9 Gad1 2.65769480702933e-118 2.57736171196825 0.518 0.016 8.25293968426818e-114
9 Gad2 4.45565666964153e-115 2.15300676054965 0.339 0.005 1.38361506562379e-110
9 Sst 3.80245898927728e-106 3.43362029816464 0.375 0.008 1.18077758994027e-101
9 Npas1 3.85160280625962e-106 1.88602382917949 0.286 0.003 1.1960382194278e-101
9 Grin2d 4.98511435151006e-79 1.57310073733633 0.268 0.005 1.54802755957442e-74
9 Slc6a1 4.65112927290534e-78 2.5271115362313 0.518 0.028 1.4443151731153e-73
9 Maf 1.91752019697663e-66 2.44936802208869 0.393 0.018 5.95447546767152e-62
9 Npy 1.88985119996317e-62 4.00205080117528 0.286 0.009 5.86855493124564e-58
9 Cacna2d2 8.04286978110743e-55 1.77386257046686 0.339 0.017 2.49755235312729e-50
9 Reln 8.39834112650569e-46 2.38318241318638 0.304 0.017 2.60793687001381e-41
10 C1qc 0 5.3550956425776 0.85 0.005 0
10 Csf1r 0 5.24878369954777 0.875 0.007 0
10 Selplg 0 5.24455077256244 0.775 0.004 0
10 Cx3cr1 0 5.11224751268857 0.825 0.006 0
10 C1qa 2.56204838981867e-307 5.97710562271564 0.975 0.012 7.95592886490392e-303
10 Siglech 5.1579034791222e-285 4.12957832635282 0.625 0.002 1.60168376737182e-280
10 Adap2os 3.27498926803563e-283 3.57990041670087 0.525 0 1.0169824174031e-278
10 Ctss 9.69114308906392e-272 4.87388626851933 0.675 0.004 3.00939066344702e-267
10 Arhgap45 2.59486668150855e-271 4.25320071716118 0.6 0.002 8.0578395060885e-267
10 Vsir 8.56724267604741e-268 4.01866506595416 0.625 0.003 2.660385868193e-263
11 Rgs9 1.67947039722311e-115 4.14472533637521 0.743 0.027 5.21525942449691e-111
11 Gpr88 5.06510975205677e-74 3.15381482905491 0.571 0.026 1.57286853130619e-69
11 Ppp1r1b 9.25722298263154e-69 3.14194224722438 0.543 0.025 2.87464545279657e-64
11 Scn4b 5.09278465971975e-63 2.65740597982115 0.457 0.019 1.58146242038277e-58
11 Rasgrp2 1.71558038094437e-58 2.1898296299182 0.314 0.009 5.32739175694654e-54
11 Adcy5 6.32583286285994e-53 3.259440345389 0.6 0.044 1.9643608789039e-48
11 Gprin3 2.00749993421538e-42 2.58072168406578 0.4 0.023 6.23388954571903e-38
11 Gng7 1.88063477897671e-37 2.08631921578334 0.314 0.016 5.83993517915637e-33
11 Penk 5.2819927668653e-36 2.96716509216199 0.343 0.02 1.64021721389468e-31
11 Pde1b 6.47234800509738e-36 3.09849032567765 0.571 0.061 2.00985822602289e-31



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.