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1k Brain Nuclei from an E18 Mouse

Nuclei 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
1442 36619 2240 52805264 98.1 57.7 97.3 97.7 94.1 90.1 2.7 20.4 67.0 63.8 1.4 86.1 16849 5836

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 Gria2 2.91235295127374e-59 1.8381676320416 0.891 0.61 9.04372961959034e-55
0 Neurod2 2.22235152132022e-42 1.16656777439504 0.862 0.552 6.90106817915567e-38
0 Vim 8.64386336195471e-33 -2.58676024747679 0.152 0.536 2.6841788897878e-28
0 Neurod6 4.70728630194881e-32 0.965127535075659 0.873 0.567 1.46175361534416e-27
0 Pou3f2 4.71810639538944e-30 1.20109759707824 0.667 0.412 1.46511357896028e-25
0 Dbi 1.45776058896885e-22 -2.60050113146087 0.446 0.72 4.52678395692496e-18
0 Sox2 2.29242356199918e-20 -0.77407416966313 0.018 0.281 7.11866288707607e-16
0 Phgdh 5.14325472769791e-20 -1.42096228147901 0.018 0.275 1.59713489059203e-15
0 Ezr 9.34681592184937e-20 -0.880986221751528 0.152 0.449 2.90246674821188e-15
0 Ndrg2 1.66761404104909e-19 -1.01431707814063 0.062 0.335 5.17844188166974e-15
1 Aldoc 2.40765936534606e-166 3.15808790180369 0.753 0.059 7.47650462720913e-162
1 Phgdh 2.56604860822856e-148 2.66650495384977 0.771 0.098 7.96835074313214e-144
1 Mt3 5.39709767932182e-137 3.79743997981537 0.855 0.215 1.6759607423598e-132
1 Ddah1 5.40588702957416e-135 2.61145161629942 0.742 0.102 1.67869009929366e-130
1 Mfge8 9.30542212449336e-135 2.34846484753402 0.647 0.051 2.88961273231892e-130
1 Dbi 7.281295526523e-133 3.71733402942854 0.982 0.593 2.26106069985119e-128
1 Sparc 9.44844979680382e-133 2.33810741518222 0.571 0.025 2.93402711540149e-128
1 Vim 7.86942971476919e-132 3.30828814407559 0.931 0.352 2.44369400932728e-127
1 Hes1 9.08793794962001e-125 2.1204486374582 0.553 0.029 2.8220773714955e-120
1 Fabp7 1.11984403201447e-118 4.91544356328212 0.935 0.505 3.47745167261452e-114
2 Ntm 1.21887796510106e-113 1.54042000202989 0.884 0.204 3.78498174502833e-109
2 Opcml 1.63076270592297e-94 1.9758926288956 0.742 0.163 5.06400743070261e-90
2 Cntn2 3.81449463024186e-87 1.33040121201955 0.936 0.311 1.184515017529e-82
2 Islr2 2.39135099509914e-77 1.24595868994024 0.734 0.178 7.42586224508137e-73
2 Dab1 4.40183008802899e-75 1.17445647540951 0.745 0.21 1.36690029723564e-70
2 Syt4 3.47525140353342e-73 1.15612239715537 0.783 0.231 1.07916981833923e-68
2 Uchl1 7.62000790939748e-71 1.15134433621575 0.996 0.721 2.3662410561052e-66
2 Gabra2 6.23237030151643e-69 1.07473468795527 0.757 0.22 1.9353379497299e-64
2 Nrp1 4.61821126050848e-67 1.1304864640293 0.921 0.365 1.4340931427257e-62
2 Runx1t1 3.31158141018056e-66 0.959121347367305 0.715 0.178 1.02834537530337e-61
3 Mfap4 3.91356184475577e-77 1.47611760424456 0.758 0.188 1.21527835965201e-72
3 Eomes 7.87387667316799e-69 1.75698664415891 0.616 0.129 2.44507492331886e-64
3 Sstr2 8.69127417661553e-69 1.42056084089647 0.749 0.22 2.69890137006442e-64
3 Rnd2 6.07535570212651e-65 1.39403507477729 0.782 0.261 1.88658020618134e-60
3 Mfng 4.67407649131608e-60 1.18189155696722 0.64 0.161 1.45144097284838e-55
3 Ezr 2.6741056261967e-54 1.21822030463334 0.815 0.319 8.30390020102861e-50
3 Pcp4 2.34481703597005e-48 1.65150843830018 0.659 0.218 7.28136034179779e-44
3 Mdk 3.74640523238361e-46 1.32551433551689 0.919 0.58 1.16337121681208e-41
3 Igsf8 1.99725311290092e-42 1.05341618927006 0.825 0.417 6.20207009149123e-38
3 Cdk2ap1 2.91878984517314e-39 0.905202602314877 0.787 0.374 9.06371810621614e-35
4 Nrxn3 1.57097275314305e-209 3.34813641815467 0.859 0.033 4.87834169033512e-205
4 Dlx2 5.27211262076286e-159 2.16881217055804 0.588 0.008 1.63714913212549e-154
4 Gad2 3.72158490566113e-157 2.40103157097575 0.647 0.02 1.15566376075495e-152
4 Maf 1.4635963167629e-135 2.65775906644725 0.612 0.028 4.54490564244384e-131
4 Dlx1 2.56535220860925e-134 2.17453720976991 0.535 0.013 7.96618821339432e-130
4 Dlx6os1 2.08661199744732e-128 2.03436181273405 0.494 0.009 6.47955623567316e-124
4 Lhx6 7.99028101304119e-125 2.08947783804412 0.476 0.008 2.48122196297968e-120
4 Gad1 3.29461343867272e-95 1.50120325823072 0.371 0.006 1.02307631111104e-90
4 Nxph1 2.36824001741817e-85 1.62918747157671 0.347 0.008 7.35409572608865e-81
4 Meg3 2.41454915742348e-84 3.42889226567418 0.9 0.318 7.49789949854712e-80
5 Ifi203 1.25430673965555e-86 0.692929195747845 0.41 0.012 3.89499871865236e-82
5 Mndal 7.12028871451866e-82 0.716941700194033 0.52 0.031 2.21106325451948e-77
5 Tbata 2.92589722345336e-74 0.44862861819836 0.29 0.004 9.08578864798972e-70
5 Lhx9 8.6415905710369e-66 0.750448349887463 0.49 0.039 2.68347312002409e-61
5 Rerg 3.53601484685033e-62 0.509080363461451 0.31 0.01 1.09803869039243e-57
5 Calb2 1.03285393966806e-57 1.66003649644597 0.58 0.071 3.20732133885123e-53
5 Kcnk1 4.77926712145354e-53 0.63658064520642 0.39 0.031 1.48410581922497e-48
5 Neurod1 1.52051537652892e-51 1.50580613213725 0.85 0.211 4.72165639873525e-47
5 Zfp385b 1.02868800498464e-49 0.262242468861399 0.27 0.011 3.1943848618788e-45
5 Synpr 6.72636414197107e-47 0.539043466977927 0.37 0.031 2.08873785700628e-42
6 Kifc1 9.54146825393219e-93 0.902956861835436 0.629 0.032 2.96291213689356e-88
6 Kif20a 1.67344190158692e-77 0.634037375598381 0.529 0.026 5.19653913699788e-73
6 Ccna2 1.6012499049721e-75 1.3803461381724 0.829 0.087 4.97236132990987e-71
6 Birc5 4.69624366495543e-74 1.89105607101382 0.871 0.106 1.45832454527861e-69
6 Cenpe 1.10344463193686e-73 1.03228254169172 0.671 0.054 3.42652661555354e-69
6 Clspn 2.49676847604975e-73 0.57860368467965 0.529 0.029 7.7532151486773e-69
6 Pclaf 2.44724688404253e-70 2.13680883233737 0.929 0.135 7.59943574901728e-66
6 Spc25 3.37294301312655e-70 1.61905205572056 0.757 0.079 1.04739999386619e-65
6 Neil3 5.54804025654829e-69 0.677277435518847 0.557 0.036 1.72283294086594e-64
6 Ska1 9.12742478151095e-69 0.71666266753773 0.571 0.039 2.8343392174026e-64
7 Alas2 1.35697490354565e-188 3.45867430836762 0.655 0.002 4.21381416798031e-184
7 Hba-a1 1.76870121121501e-151 9.66808653789585 0.964 0.042 5.49234787118598e-147
7 Hbb-bt 4.60013128990868e-151 8.60181786798022 0.964 0.042 1.42847876945534e-146
7 Hba-a2 3.63252223056914e-142 9.5888607015222 0.964 0.048 1.12800712825863e-137
7 Hbb-bs 9.00623265774082e-61 10.0421401496446 0.964 0.197 2.79670542720826e-56
7 Ube2l6 3.00804774530557e-46 2.11694259927158 0.545 0.056 9.34089066349739e-42
7 Eef1a1 2.72149928039077e-35 -4.29225198716681 0.418 0.991 8.45107171539745e-31
7 Tuba1a 5.21866203634301e-35 -5.76391201070184 0.2 0.991 1.62055112214559e-30
7 Rps8 6.80830945300702e-35 -4.11218773216002 0.291 0.986 2.11418433444227e-30
7 Rpl14 6.99016586347659e-35 -4.21665987365811 0.091 0.981 2.17065620558539e-30
8 Lhx1os 2.55069318254564e-231 2.05583231404331 0.833 0.001 7.92066753975897e-227
8 Trp73 2.75707815209185e-219 1.25519115778562 0.833 0.002 8.56155478569081e-215
8 Gdf5 1.72448550097415e-204 1.82643448666118 0.889 0.004 5.35504482617502e-200
8 Lhx5 7.51894645160276e-197 1.77608638744023 0.833 0.004 2.3348584416162e-192
8 Gm27199 3.71558550676086e-176 1.28588450446607 0.611 0.001 1.15380076741445e-171
8 Ndnf 5.29402131799917e-157 2.1267772838127 0.667 0.003 1.64395243987828e-152
8 Lhx1 1.09559812693011e-132 1.18291679073065 0.611 0.004 3.40216086355608e-128
8 Mab21l1 3.93498530959967e-129 1.11888541413184 0.5 0.001 1.22193098818999e-124
8 Barhl2 5.17813696134129e-129 0.690938215510339 0.5 0.001 1.60796687060531e-124
8 Cacna2d2 4.087459648836e-119 2.14759725167016 0.833 0.013 1.26927884475304e-114



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.