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9k Brain Cells from an E18 Mouse

Cells from cortex, hippocampus and subventricular zone of an E18 mouse. (9k cells are increased to 11k from CellRanger v3.1 onwards)

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
11277 33995 2315 383366284 98.3 65.5 98.3 98.2 95.2 92.2 2.8 21.8 67.6 64.0 1.8 86.0 20236 5585

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 Neurod2 0 1.20569349530486 0.99 0.521 0
0 Gpm6a 0 1.18231473073607 0.97 0.665 0
0 Satb2 0 1.13237043040811 0.677 0.137 0
0 Bcl11a 0 1.12884872162177 0.934 0.587 0
0 Bhlhe22 0 1.12631932256717 0.851 0.329 0
0 Hs6st2 0 1.10379375104502 0.662 0.163 0
0 Dab1 0 1.08447555240334 0.715 0.241 0
0 Neurod6 0 1.04377343434255 0.982 0.542 0
0 Ttc28 0 0.999783072831358 0.945 0.554 0
0 Dok5 0 0.978200950940457 0.73 0.288 0
1 Pcp4 0 1.40294765063465 0.72 0.243 0
1 Meis2 0 1.31659714842668 0.993 0.615 0
1 Sstr2 0 1.29328093857601 0.633 0.179 0
1 Unc5d 0 1.17751369433046 0.66 0.18 0
1 Ppp2r2b 0 1.14228006390317 0.904 0.516 0
1 Rnd2 2.15169299557064e-295 1.10687323505059 0.62 0.213 6.6816522591455e-291
1 Tagln3 9.00488173574917e-261 0.906659762184565 0.961 0.686 2.79628592540219e-256
1 Pou3f2 7.07731585402761e-254 0.99261581939047 0.785 0.37 2.19771889215119e-249
1 Ldhb 2.3248539816809e-235 0.849903609364657 0.936 0.657 7.21936906931369e-231
1 Sema3c 1.37940012446554e-229 0.709853075553128 0.809 0.354 4.28345120650285e-225
2 Nrxn3 0 2.79444222891355 0.826 0.066 0
2 Adarb2 0 2.36794679405378 0.297 0.015 0
2 Dlx1 0 2.19038787586465 0.58 0.042 0
2 Dlx2 0 2.18025835157695 0.648 0.04 0
2 Maf 0 2.13896295116751 0.554 0.035 0
2 Meg3 0 2.1106331779497 0.912 0.351 0
2 Dlx6os1 0 2.05013427726706 0.504 0.026 0
2 Arx 0 1.99895171140632 0.632 0.14 0
2 Gad2 0 1.89150534392621 0.553 0.036 0
2 Lhx6 0 1.86631167833322 0.44 0.023 0
3 Pgk1 6.82191287814728e-191 -0.719008815815921 0.12 0.632 2.11840860605107e-186
3 Slc25a5 2.97387836835874e-185 -0.886886326165023 0.262 0.785 9.23478449726439e-181
3 Ppp1ca 1.60101597005237e-179 -0.634656927136688 0.216 0.754 4.97163489180362e-175
3 Capza2 4.9494449018675e-171 -0.575228342820586 0.187 0.715 1.53695112537692e-166
3 Rpl3 2.59275689707419e-169 -0.699066313861325 0.676 0.955 8.05128799248447e-165
3 Rtraf 7.35117407928258e-164 -0.624996281500889 0.273 0.811 2.28276008683962e-159
3 Rpl4 1.93450585017632e-162 -0.677251162542855 0.669 0.952 6.00722101655252e-158
3 Cnbp 7.03775139864223e-160 -0.644795081513858 0.282 0.811 2.18543294182037e-155
3 H1f0 2.13889824463603e-158 -0.81319660676919 0.199 0.683 6.64192071906825e-154
3 Vdac1 2.59476937578052e-157 -0.542884739527626 0.236 0.768 8.05753734261125e-153
4 Snca 0 2.32884108791175 0.85 0.216 0
4 Zbtb20 0 2.03483912464149 0.999 0.719 0
4 Calb2 0 1.80036398068223 0.595 0.086 0
4 Crym 0 1.62045325592118 0.616 0.051 0
4 Islr2 0 1.58211324214194 0.964 0.305 0
4 Neurod1 0 1.57478204431346 0.809 0.217 0
4 S100a10 0 1.36069757196332 0.56 0.116 0
4 Rnf182 0 1.32402699651151 0.938 0.353 0
4 Grp 0 1.31676048070211 0.499 0.069 0
4 Nrxn1 0 1.30920331214619 0.912 0.34 0
5 Fabp7 0 3.65040962545615 0.995 0.736 0
5 Aldoc 0 3.34205950955373 0.94 0.122 0
5 Mt3 0 3.1785292329746 0.989 0.336 0
5 Dbi 0 3.10041874049326 1 0.688 0
5 Vim 0 2.66019435919834 0.989 0.353 0
5 Hes5 0 2.53514817676191 0.81 0.109 0
5 Id3 0 2.52949318413154 0.707 0.132 0
5 Phgdh 0 2.43755014627884 0.965 0.147 0
5 Ddah1 0 2.36599517122525 0.914 0.146 0
5 Slc1a3 0 2.35527193271837 0.976 0.241 0
6 Hmgb2 0 3.76014092294228 0.974 0.367 0
6 Ube2c 0 3.23937277112399 0.875 0.071 0
6 Cks2 0 3.12469055005944 0.888 0.131 0
6 Cenpa 0 2.79305722553305 0.793 0.063 0
6 Top2a 0 2.66811280501403 0.743 0.04 0
6 Pclaf 0 2.65306337255035 0.826 0.055 0
6 Pbk 0 2.55397588870649 0.859 0.046 0
6 Cdc20 0 2.38161367080482 0.72 0.036 0
6 Birc5 0 2.34516441680362 0.829 0.045 0
6 Ccnb1 0 2.34041642018158 0.716 0.025 0
7 Nefl 0 1.60076960386392 0.368 0.02 0
7 Ndrg1 0 0.893629423688795 0.516 0.061 0
7 Sla 0 0.869295551526753 0.413 0.033 0
7 Ldb2 1.64402044771407e-289 0.882006073797353 0.415 0.042 5.10517669628651e-285
7 Nefm 8.66575018977482e-259 1.0461414905691 0.371 0.038 2.69097540643078e-254
7 Lrfn5 3.31425399880381e-244 0.918953394237041 0.504 0.076 1.02917529424855e-239
7 Tshz3 4.78131292954569e-234 0.700087164416624 0.346 0.035 1.48474110401182e-229
7 Mef2c 5.61373726599347e-227 1.81845395621147 0.893 0.309 1.74323383320895e-222
7 Dync1i1 2.02555551293232e-218 0.832490471794813 0.424 0.059 6.28995753430874e-214
7 Tshz2 1.7614114600447e-215 1.2293874987806 0.413 0.059 5.46971100687681e-211
8 Neurog2 0 2.5342975616965 0.842 0.178 0
8 Eomes 0 2.45920127038083 0.938 0.122 0
8 Mfap4 0 2.39114909316664 0.918 0.166 0
8 Btbd17 0 1.57070425437147 0.803 0.128 0
8 Neurod4 0 0.62363553718206 0.313 0.016 0
8 Mfng 5.28228622732907e-290 1.27801609683052 0.703 0.136 1.6403083421725e-285
8 Tac2 5.19098086105355e-232 1.86864081585492 0.315 0.029 1.61195528678296e-227
8 Mdk 7.90108842691879e-219 1.64825343878406 0.982 0.554 2.45352498921109e-214
8 Ezr 1.51759145253725e-217 1.47257081224658 0.883 0.322 4.71257673756392e-213
8 Igsf8 4.65207115550088e-202 1.36406044973231 0.896 0.383 1.44460765591769e-197
9 Tnc 5.74871632328915e-158 3.95099729641705 0.571 0.123 1.78514887987098e-153
9 Mfge8 2.49719153278268e-108 3.03807896025155 0.588 0.185 7.75452886675004e-104
9 Atp1a2 1.71235093219725e-107 2.45339217480921 0.503 0.13 5.31736334975211e-103
9 Tubb3 7.67759477775765e-106 -2.13345189722257 0.326 0.883 2.38412350633708e-101
9 Sox11 2.38195809283469e-100 -2.07126849457724 0.374 0.904 7.39669446567956e-96
9 Sox4 2.20898158015638e-99 -1.856009034763 0.306 0.893 6.85955050085961e-95
9 Cd24a 2.30762664821085e-99 -1.88443839108873 0.297 0.889 7.16587303068917e-95
9 Apoe 7.62711288353908e-99 2.99643196293296 0.632 0.234 2.36844736372539e-94
9 Tubb5 1.37535480452689e-98 -1.46620759629682 0.659 0.968 4.27088927449734e-94
9 Basp1 1.51813318366024e-97 -1.85842949869772 0.168 0.814 4.71425897522015e-93
10 Olig2 0 2.27795949223036 0.631 0.046 0
10 Pdgfra 0 1.29765350455292 0.328 0.009 0
10 Olig1 6.12310976832949e-287 3.4873710350496 0.634 0.064 1.90140927635936e-282
10 Smoc1 7.89921978562094e-168 0.805993148613275 0.358 0.031 2.45294472002887e-163
10 Sox8 9.09792360181809e-158 1.05193524419287 0.47 0.059 2.82517821607257e-153
10 Mcm3 1.55984220636399e-152 1.04547958398888 0.485 0.066 4.84377800342209e-148
10 C1ql1 1.67988232075614e-151 0.879498107832166 0.306 0.025 5.21653857064404e-147
10 Ung 1.38225118043761e-147 1.05787645059838 0.451 0.058 4.29230459061292e-143
10 Ccnd1 1.02147418293175e-137 1.08039983605553 0.496 0.074 3.17198378025798e-133
10 Uhrf1 1.3621296895368e-129 0.830331158783276 0.44 0.062 4.22982132491864e-125
11 Snhg11 0 4.527084174781 0.794 0.041 0
11 Reln 0 4.50320457252921 0.978 0.04 0
11 Nhlh2 0 3.19992552968522 0.879 0.092 0
11 Ndnf 0 2.58458837803375 0.785 0.005 0
11 Cacna2d2 0 2.47119895926558 0.798 0.026 0
11 Lhx1os 0 2.21188434675883 0.677 0.005 0
11 Gm28050 0 1.98321366352138 0.637 0.026 0
11 Rgs4 0 1.90208748927235 0.677 0.03 0
11 Trp73 0 1.85058284534452 0.677 0.003 0
11 Lhx5 0 1.84493390004952 0.695 0.003 0
12 Hbb-bt 0 7.57034265429069 1 0.112 0
12 Alas2 0 3.62325153690981 0.689 0.006 0
12 Hba-a1 5.80100600447089e-228 8.64491403878276 1 0.173 1.80138639456835e-223
12 Ube2l6 2.08718814776881e-204 2.53450279578109 0.59 0.05 6.48134535526649e-200
12 Hba-a2 1.86700486529897e-186 8.48063948954048 1 0.229 5.79761020821288e-182
12 Hbb-bs 1.65171173848075e-124 8.5874723027135 1 0.455 5.12906046150426e-120
12 Malat1 2.73439832491044e-97 -5.28509779797971 0.416 0.977 8.4911271183444e-93
12 Actg1 2.86332600601303e-95 -3.6346939365392 0.373 0.976 8.89148624647226e-91
12 Ptma 1.02255611988918e-94 -3.42091671631224 0.516 0.982 3.17534351909188e-90
12 Eef1a1 2.28924679240744e-92 -2.93374093862624 0.671 0.979 7.10879806446283e-88
13 Cldn5 0 6.05021034932752 0.958 0.026 0
13 Igfbp7 0 4.52963713831394 0.854 0.024 0
13 Itm2a 0 3.99594775188478 0.812 0.041 0
13 Egfl7 0 3.424343103753 0.799 0.036 0
13 Vwa1 0 3.41266500002248 0.799 0.013 0
13 Pglyrp1 0 3.37206732175683 0.799 0.015 0
13 Flt1 0 3.25304755805151 0.785 0.005 0
13 Gng11 0 3.18224385264187 0.757 0.026 0
13 Ctla2a 0 3.15517823229278 0.743 0.008 0
13 Apod 0 3.06811168387906 0.681 0.011 0
14 Ccl4 0 5.55093642573741 0.67 0.011 0
14 C1qb 0 5.35159790462755 0.896 0.006 0
14 C1qc 0 5.18158592491754 0.953 0.005 0
14 C1qa 0 5.03700236945892 0.896 0.005 0
14 Tyrobp 0 4.95942513130699 0.962 0.005 0
14 Ccl3 0 4.9494312804055 0.698 0.007 0
14 Hexb 0 4.61993095692559 0.896 0.032 0
14 Fcer1g 0 4.3777122022958 0.906 0.004 0
14 Fcrls 0 4.20776430061056 0.858 0.002 0
14 Crybb1 0 4.1327264486524 0.802 0.004 0
15 Rgs5 0 5.65952773660613 0.902 0.038 0
15 Vtn 0 4.85269876683333 0.976 0.008 0
15 Higd1b 0 4.85065977015411 0.878 0.01 0
15 Igfbp7 0 4.51904901763028 0.963 0.028 0
15 Ndufa4l2 0 4.40691620975431 0.951 0.011 0
15 Kcnj8 0 4.02538038063782 0.902 0.006 0
15 Gng11 0 4.01887034888765 0.951 0.028 0
15 Bgn 0 3.74685910061684 0.963 0.016 0
15 Col4a1 0 3.65049414951712 0.89 0.031 0
15 Dlk1 0 3.6104769572817 0.78 0.01 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.