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2k Fixed (for 6 days at -80ºC) Brain Cells from an E18 Mouse

Cells from a combined cortex, hippocampus and sub ventricular zone of an E18 mouse. Cells were fixed, stored at -80ºC for 6 days, and then rehydrated.

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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
2520 81351 1251 205004798 97.6 92.9 98.1 98.1 89.6 83.6 2.3 10.5 70.9 67.8 1.2 85.6 16685 2262

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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 1.47125894961477e-113 1.51322741759866 0.882 0.451 4.56870041623874e-109
0 Syt4 3.44173323333749e-102 1.35498056287738 0.518 0.109 1.06876142094829e-97
0 Cd24a 4.41772207604881e-97 1.04602228629698 0.974 0.707 1.37183523627544e-92
0 Neurod2 3.05080313408966e-90 1.00825023081447 0.852 0.357 9.47365897228862e-86
0 Cntn2 2.52663011037792e-87 1.15615737443536 0.618 0.186 7.84594448175657e-83
0 Stmn4 7.38067813525983e-84 1.09144977726203 0.878 0.435 2.29192198134224e-79
0 Bcl11a 1.23988333771474e-82 1.07519536960181 0.792 0.354 3.85020972860557e-78
0 Stmn2 2.30697087332783e-82 1.01134634228982 0.917 0.486 7.16383665294491e-78
0 Mllt11 2.49404558977341e-81 1.00811774259025 0.911 0.511 7.74475976992338e-77
0 Neurod6 1.19928247737001e-79 1.04209707211623 0.934 0.489 3.7241318769771e-75
1 Eomes 3.97458599742219e-83 1.3576972999161 0.369 0.058 1.23422818977951e-78
1 Mfap4 1.81188923127665e-70 1.34870226098262 0.496 0.14 5.62645962988338e-66
1 Mdk 2.98803882970017e-68 1.14888974399845 0.895 0.547 9.27875697786794e-64
1 Sstr2 1.55398030165511e-62 1.05108154930776 0.354 0.074 4.82557503072962e-58
1 Pcp4 8.63840476093528e-61 1.46968894845974 0.562 0.219 2.68248383041323e-56
1 Rnd2 5.88915107228426e-60 1.1635863225006 0.466 0.142 1.82875808247643e-55
1 Mfng 6.36911918834088e-57 0.948186322657457 0.41 0.111 1.97780258155549e-52
1 Ezr 5.62520375061396e-55 1.12933513200295 0.491 0.177 1.74679452067815e-50
1 Elavl2 8.8069270620555e-51 0.954886374531975 0.607 0.257 2.73481506058009e-46
1 Igsf8 2.11009247962366e-48 1.04058050885871 0.567 0.25 6.55247017697535e-44
2 Cst3 2.00492312656682e-29 -0.95377957241782 0.298 0.685 6.22588778492795e-25
2 Pgk1 4.72507799030767e-28 -0.794472868768081 0.107 0.414 1.46727846833024e-23
2 Pfn2 1.63372325692391e-27 -0.81539304222242 0.241 0.597 5.0732008297258e-23
2 Eno1 3.81112632025025e-25 -0.582423711954105 0.23 0.578 1.18346905622731e-20
2 Vim 3.9176119898285e-25 -1.11298388460216 0.107 0.379 1.21653605120144e-20
2 Fxyd6 1.91790336832075e-24 -0.633814918042598 0.203 0.533 5.95566532964642e-20
2 Pgam1 2.23631427956782e-24 -0.639784207977166 0.162 0.475 6.94442673234195e-20
2 Ywhae 2.66177356048901e-24 -0.557499975776732 0.522 0.848 8.26560543738652e-20
2 Tspan3 4.49548206108494e-24 -0.526775279799316 0.214 0.558 1.39598204442871e-19
2 Hnrnpf 4.78743949630825e-24 -0.608383249811577 0.173 0.488 1.4866435867886e-19
3 Meg3 2.36179879962601e-128 2.44147773386284 0.77 0.219 7.33409381247863e-124
3 Nrxn3 1.18038013090491e-127 2.28235958534043 0.388 0.027 3.66543442049903e-123
3 Dlx5 2.14534888171666e-95 2.07619340656239 0.347 0.034 6.66195188239474e-91
3 Sp9 1.62592859789834e-88 2.01071318530577 0.321 0.031 5.04899607505372e-84
3 Dlx6os1 9.05416928695457e-83 1.76860671404071 0.294 0.027 2.811591188678e-78
3 Dlx2 2.35296336110743e-81 1.90760829537718 0.321 0.036 7.30665712524689e-77
3 Dlx1 1.22003298930477e-70 1.94985155383676 0.292 0.035 3.78856844168811e-66
3 Neurod6 2.13550598248335e-60 -2.02764614959492 0.143 0.654 6.63138672740554e-56
3 Zbtb18 1.27905431901846e-44 -1.47765035858242 0.102 0.552 3.97184737684802e-40
3 Ptn 2.48901307717184e-43 -1.94482439070335 0.213 0.627 7.72913230854172e-39
4 Pclaf 3.4670790461318e-201 2.45649391142887 0.713 0.065 1.07663205619531e-196
4 Cdk1 3.63946315701327e-201 2.08525360561048 0.64 0.043 1.13016249414733e-196
4 Rrm2 3.95208699052256e-197 1.95494872539176 0.651 0.047 1.22724157316697e-192
4 Top2a 1.36630732128976e-187 1.77842089598671 0.533 0.025 4.24279412480109e-183
4 Spc24 3.1378836912012e-183 1.77161514183806 0.676 0.061 9.74407022628708e-179
4 Ccna2 1.41263324833537e-175 1.63346652269585 0.489 0.021 4.38665002605584e-171
4 Tpx2 5.13473790410164e-175 1.54931978394672 0.504 0.024 1.59449016136068e-170
4 Pbk 1.12087489054488e-169 2.06449819162723 0.621 0.056 3.48065279760901e-165
4 Hmgb2 7.01371081405478e-168 3.29190936872009 0.967 0.335 2.17796761908843e-163
4 Birc5 1.22471161341176e-167 1.97273855525132 0.643 0.063 3.80309697312753e-163
5 Aldoc 1.56506098464422e-139 2.92032501027082 0.786 0.132 4.85998387561569e-135
5 Phgdh 4.97526176212582e-121 2.52824098321805 0.8 0.169 1.54496803499293e-116
5 Tnc 7.97383614039684e-120 2.71445611627606 0.633 0.087 2.47611533667743e-115
5 Vim 2.73932967894363e-109 2.48135311137397 0.895 0.281 8.50644045202366e-105
5 Dbi 2.26806146882867e-105 2.88063677157017 0.986 0.72 7.04301127915368e-101
5 Mt3 3.26046095562275e-103 3.29365232234624 0.924 0.404 1.01247094054953e-98
5 Mfge8 6.79873553143562e-102 2.33548847068609 0.738 0.159 2.1112113445767e-97
5 Mt2 1.65121165936942e-101 2.75829350949398 0.743 0.173 5.12750756583985e-97
5 Mt1 2.38432503264146e-99 2.79573005460372 0.79 0.221 7.40404452386153e-95
5 Slc1a3 4.87563565139297e-95 1.92168969721172 0.61 0.106 1.51403113882706e-90
6 Crym 8.62536499046835e-88 1.67018000589872 0.452 0.035 2.67843459049014e-83
6 Calb2 3.62898994226551e-76 2.28121466873991 0.524 0.062 1.12691024677171e-71
6 Snca 6.94549853607253e-76 2.16411161013121 0.661 0.106 2.1567856604066e-71
6 Nrp2 4.02483701443651e-68 0.879447538198085 0.29 0.016 1.24983263809297e-63
6 Nhlh2 4.7007324970156e-66 1.30325405069613 0.29 0.018 1.45971846229826e-61
6 Islr2 1.13292783021637e-61 1.50914516776605 0.694 0.131 3.51808079117088e-57
6 Neurod1 3.12958745079871e-61 1.69073864807557 0.637 0.114 9.71830791096523e-57
6 Camk2b 1.25436714373156e-51 0.973051167606243 0.452 0.063 3.89518629142962e-47
6 Zbtb20 9.8722433935509e-48 1.80585941343614 0.935 0.412 3.06562774099936e-43
6 Gap43 4.62607686849059e-46 1.94674237391625 0.847 0.311 1.43653564997238e-41
7 Alas2 2.94065564241857e-210 4.15163124447175 0.775 0.026 9.13161796640238e-206
7 Ube2l6 2.46873401131146e-105 2.46090581673854 0.55 0.032 7.66615972532547e-101
7 Hbb-bt 5.96595594938376e-53 5.93748578916888 1 0.73 1.85260830096214e-48
7 mt-Atp6 7.19584512327041e-51 -4.095013578323 0.412 0.995 2.23452578612916e-46
7 Tmsb10 1.37198658312801e-50 -4.15835203255549 0.412 0.998 4.2604299365874e-46
7 Malat1 2.29186740842543e-50 -5.62963746889202 0.262 0.986 7.11693586338349e-46
7 Tmsb4x 2.82053437100743e-50 -4.01135099457779 0.5 0.998 8.75860538228936e-46
7 mt-Co3 3.02075499938481e-50 -3.62476370398929 0.475 0.995 9.38035049958965e-46
7 Stmn1 5.09239510815571e-50 -3.97696626368591 0.4 0.993 1.58134145293559e-45
7 Tuba1a 2.74749170890066e-49 -3.99037355081415 0.512 0.993 8.53178600364922e-45
8 Foxf2 1.93047373456367e-210 2.12312193002512 0.477 0.002 5.99470008794057e-206
8 Selenop 1.11321321309057e-180 3.52890444073163 0.682 0.013 3.45686099061015e-176
8 Col4a1 4.28572109204853e-176 3.08220063016438 0.568 0.008 1.33084497071383e-171
8 Col4a2 4.08914019612559e-170 2.9115449046174 0.591 0.009 1.26980070510288e-165
8 Laptm5 2.48442169386467e-165 3.45500284225724 0.432 0.003 7.71487468595796e-161
8 Eng 2.67728788043422e-149 2.4038515761263 0.386 0.003 8.31378205511239e-145
8 Slc40a1 1.30620436285351e-148 1.96700893054089 0.386 0.003 4.05615640796901e-144
8 BC028528 3.04260517098481e-148 1.8831639229093 0.409 0.004 9.44820183745913e-144
8 Slc22a8 5.62989435050928e-144 1.92949186799212 0.364 0.002 1.74825109266365e-139
8 Slco2b1 5.03229378442178e-143 1.29143522699255 0.318 0.001 1.5626781888765e-138



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.