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Estimated Number of Cells

2,352

Mean Reads per Cell

50,485

Median Genes per Cell

775

Sequencing

Number of Reads 118,742,315
Valid Barcodes 97.4%
Sequencing Saturation 83.3%
Q30 Bases in Barcode 98.3%
Q30 Bases in RNA Read 67.9%
Q30 Bases in Sample Index 94.0%
Q30 Bases in UMI 98.1%

Mapping

Reads Mapped to Genome 81.1%
Reads Mapped Confidently to Genome 79.3%
Reads Mapped Confidently to Intergenic Regions 6.9%
Reads Mapped Confidently to Intronic Regions 46.0%
Reads Mapped Confidently to Exonic Regions 26.3%
Reads Mapped Confidently to Transcriptome 23.5%
Reads Mapped Antisense to Gene 1.9%
 

Cells

Cells
CellsBackground
Estimated Number of Cells 2,352
Fraction Reads in Cells 70.0%
Mean Reads per Cell 50,485
Median Genes per Cell 775
Total Genes Detected 17,059
Median UMI Counts per Cell 1,127

Sample

Name nuclei_2k
Description Nuclei from a combined cortex, hippocampus and subventricular zone of an adult mouse (>8 weeks)
Transcriptome mm10
Chemistry Single Cell 3' v2
Cell Ranger Version 2.1.0

Clustering Type:

Shown here are the total UMI counts for each cell-barcode. Cells with greater UMI counts likely have higher RNA content than cells with fewer UMI counts. The axes correspond to the 2-dimensional embedding produced by the t-SNE algorithm. In this space, pairs of cells that are close to each other have more similar gene expression profiles than cells that are distant from each other. The display is limited to a random subset of 10000 cells.

t-SNE Projection of Cells Colored by UMI Counts

UMI counts: 1,098
5001000150020002500
 
These are the assignments of each cell-barcode a clusters by an automated clustering algorithm. The clustering groups together cells that have similar expression profiles. The axes correspond to the 2-dimensional embedding produced by the t-SNE algorithm. In this space, pairs of cells that are close to each other have more similar gene expression profiles than cells that are distant from each other. The display is limited to a random subset of 10000 cells and K-means up to K=20. Please use Loupe(tm) Cell Browser to view the entire dataset.

t-SNE projection of Cells Colored by Automated Clustering

1 - 468 cells 2 - 415 cells 3 - 384 cells 4 - 381 cells 5 - 344 cells 6 - 300 cells 7 - 60 cells
The differential expression analysis seeks to find, for each cluster, genes that are more highly expressed in that cluster relative to the rest of the sample. Here a differential expression test was performed between each cluster and the rest of the sample for each gene. The Log2 fold-change (L2FC) is an estimate of the log2 ratio of expression in a cluster to that in all other cells. A value of 1.0 indicates 2-fold greater expression in the cluster of interest. The p-value is a measure of the statistical significance of the expression difference and is based on a negative binomial test. The p-value reported here has been adjusted for multiple testing via the Benjamini-Hochberg procedure. In this table you can click on a column to sort by that value. Also, in this table genes were filtered by (Mean UMI counts > 1.0) and the top N genes by L2FC for each cluster were retained. Genes with L2FC < 0 or adjusted p-value >= 0.10 were grayed out. The number of top genes shown per cluster, N, is set to limit the number of table entries shown to 10000; N=10000/K^2 where K is the number of clusters. N can range from 1 to 50. For the full table, please refer to the "differential_expression.csv" files produced by the pipeline.

Top Genes By Cluster (Log2 fold-change, p-value)

    Cluster 1Cluster 2Cluster 3Cluster 4Cluster 5Cluster 6Cluster 7  

Gene ID

Gene name

L2FC

p-value

L2FC

p-value

L2FC

p-value

L2FC

p-value

L2FC

p-value

L2FC

p-value

L2FC

p-value

ENSMUSG00000001986Gria3 0.798e-02-0.071e+00-3.071e-06-0.261e+00-0.388e-010.431e+00-2.341e+00
ENSMUSG00000005583Mef2c 0.712e-01-0.051e+00-2.369e-051.071e-02-2.361e-08-0.001e+00-2.701e+00
ENSMUSG00000044573Acp1 0.623e-01-1.943e-02-5.386e-130.151e+001.006e-03-0.841e+00-0.681e+00
ENSMUSG00000028248Pnisr 0.593e-01-0.721e+00-3.351e-070.409e-010.121e+00-0.281e+000.281e+00
ENSMUSG00000030428Ttyh1 0.584e-01-0.821e+00-1.707e-030.469e-01-0.852e-01-0.071e+002.103e-02
ENSMUSG00000010086Rnf112 0.554e-01-1.432e-01-3.583e-080.081e+000.912e-02-0.531e+00-1.721e+00
ENSMUSG00000032503Arpp21 0.534e-01-0.341e+00-2.444e-050.772e-01-0.723e-010.091e+00-1.291e+00
ENSMUSG00000059974Ntm 0.525e-01-0.221e+00-1.832e-030.606e-01-1.133e-02-0.061e+001.602e-01
ENSMUSG00000028399Ptprd 0.505e-01-0.231e+00-3.469e-081.212e-03-1.534e-040.071e+00-2.958e-01
ENSMUSG00000024109Nrxn1 0.505e-01-0.621e+00-2.721e-050.947e-02-0.319e-01-0.441e+00-0.321e+00
ENSMUSG00000025326Ube3a 0.485e-01-1.001e+00-4.142e-100.488e-010.378e-01-0.141e+00-1.221e+00
ENSMUSG00000027797Dclk1 0.465e-01-0.371e+00-3.049e-070.517e-01-0.438e-010.171e+000.681e+00
ENSMUSG00000055692Tmem191c 0.465e-01-0.751e+00-3.061e-060.339e-010.368e-01-0.071e+00-1.261e+00
ENSMUSG00000056211R3hdm1 0.436e-01-0.451e+00-3.715e-091.119e-03-0.713e-01-0.071e+00-1.731e+00
ENSMUSG00000105361AY036118 0.426e-01-0.641e+00-1.233e-020.121e+000.298e-01-0.201e+00-0.241e+00
ENSMUSG00000037266Rsrp1 0.426e-01-0.451e+00-3.063e-070.399e-010.011e+000.021e+000.351e+00
ENSMUSG00000036564Ndrg4 0.426e-01-0.471e+00-2.416e-050.458e-01-0.001e+000.101e+00-1.341e+00
ENSMUSG00000025372Baiap2 0.416e-01-0.671e+00-3.529e-080.161e+000.534e-010.041e+00-2.261e+00
ENSMUSG00000101609Kcnq1ot1 0.406e-01-0.281e+00-3.981e-090.349e-010.181e+000.061e+00-1.401e+00
ENSMUSG00000027273Snap25 0.396e-01-0.011e+00-2.004e-040.556e-01-0.487e-010.131e+00-1.811e+00
ENSMUSG00000097545Mir124a-1hg 0.396e-01-0.141e+00-3.021e-060.625e-01-0.211e+000.011e+00-1.561e+00
ENSMUSG00000034730Adgrb1 0.396e-01-0.031e+00-2.641e-050.379e-01-0.211e+000.181e+00-0.941e+00
ENSMUSG00000049583Grm5 0.396e-01-0.571e+00-2.525e-05-0.539e-010.998e-03-0.141e+00-2.351e+00
ENSMUSG00000062257Opcml 0.396e-01-0.731e+00-3.521e-07-0.431e+001.101e-03-0.281e+00-1.591e+00
ENSMUSG00000030209Grin2b 0.387e-01-1.001e+00-3.146e-07-0.321e+001.141e-03-0.391e+00-1.441e+00
ENSMUSG00000002107Celf2 0.386e-01-0.451e+00-2.939e-070.439e-010.151e+000.091e+00-1.981e+00
ENSMUSG00000021268Meg3 0.377e-01-0.161e+00-3.332e-080.359e-010.031e+000.191e+00-2.241e+00
ENSMUSG00000086503Xist 0.367e-01-0.401e+00-3.525e-090.654e-01-0.171e+000.021e+000.171e+00
ENSMUSG00000029823Luc7l2 0.357e-01-0.311e+00-3.154e-070.211e+000.289e-010.121e+00-1.021e+00
ENSMUSG00000046447Camk2n1 0.357e-01-0.081e+00-0.201e+000.488e-01-1.025e-020.101e+00-1.071e+00
ENSMUSG00000055567Unc80 0.337e-01-0.221e+00-3.582e-080.537e-01-0.021e+000.141e+00-1.651e+00
ENSMUSG00000027620Rbm39 0.337e-01-0.411e+00-3.371e-070.091e+000.426e-010.151e+00-0.601e+00
ENSMUSG00000027677Ttc14 0.328e-01-0.301e+00-2.892e-060.517e-010.041e+00-0.001e+00-0.371e+00
ENSMUSG00000031342Gpm6b 0.328e-01-0.541e+00-1.634e-030.271e+000.131e+00-0.151e+001.088e-01
ENSMUSG00000034160Ogt 0.318e-01-0.381e+00-3.116e-070.439e-010.041e+000.141e+000.161e+00
ENSMUSG00000095041PISD 0.318e-01-0.221e+00-2.502e-050.251e+000.249e-010.051e+00-1.051e+00
ENSMUSG00000097767Miat 0.318e-01-0.371e+00-3.047e-070.537e-010.141e+000.061e+00-1.861e+00
ENSMUSG00000038738Shank1 0.288e-01-0.241e+00-1.762e-03-0.021e+000.524e-01-0.061e+00-2.071e+00
ENSMUSG00000030795Fus 0.288e-01-0.141e+00-3.166e-070.241e+000.249e-010.101e+00-0.451e+00
ENSMUSG00000058254Tspan7 0.278e-01-0.361e+00-0.961e-010.081e+00-0.428e-010.161e+001.975e-02
ENSMUSG00000061751Kalrn 0.268e-01-0.431e+00-3.435e-080.919e-02-0.031e+00-0.141e+00-2.131e+00
ENSMUSG00000032936Camkv 0.268e-01-0.291e+00-2.114e-04-0.509e-010.989e-03-0.221e+00-1.951e+00
ENSMUSG00000035864Syt1 0.268e-01-0.141e+00-2.405e-050.439e-01-0.151e+000.371e+00-2.471e+00
ENSMUSG00000092341Malat1 0.268e-01-0.411e+00-3.471e-090.478e-010.338e-01-0.391e+000.931e+00
ENSMUSG00000020719Ddx5 0.258e-01-0.491e+00-2.291e-040.031e+000.563e-01-0.061e+000.351e+00
ENSMUSG00000097971Gm26917 0.258e-01-0.601e+00-1.517e-030.021e+000.298e-01-0.241e+001.827e-02
ENSMUSG00000059187Fam19a1 0.238e-01-1.681e-01-5.083e-11-0.943e-012.001e-11-1.201e+00-3.059e-01
ENSMUSG00000044349Snhg11 0.238e-01-0.101e+00-3.244e-080.517e-010.011e+000.181e+00-1.791e+00
ENSMUSG00000032826Ank2 0.228e-01-0.061e+00-2.912e-060.161e+000.239e-010.191e+00-0.141e+00
ENSMUSG00000019943Atp2b1 0.209e-01-0.511e+00-2.582e-05-0.519e-011.016e-030.071e+00-1.321e+00
ENSMUSG00000001270Ckb 0.189e-01-0.101e+00-1.078e-020.091e+00-0.517e-010.031e+002.315e-03
ENSMUSG00000032076Cadm1 0.159e-010.061e+00-2.852e-050.101e+000.031e+000.211e+001.355e-01
ENSMUSG00000028782Adgrb2 0.159e-01-0.311e+00-1.968e-04-0.101e+000.711e-01-0.001e+00-0.711e+00
ENSMUSG00000000416Cttnbp2 0.141e+00-0.791e+00-3.451e-070.141e+000.941e-02-0.071e+00-1.751e+00
ENSMUSG00000098178Gm42418 0.111e+00-0.421e+00-0.624e-01-0.081e+000.101e+00-0.311e+002.217e-03
ENSMUSG00000024617Camk2a 0.101e+00-0.301e+00-0.565e-01-0.091e+000.436e-010.071e+00-2.011e+00
ENSMUSG00000031748Gnao1 0.091e+00-0.451e+00-1.954e-030.001e+000.191e+00-0.101e+002.522e-03
ENSMUSG00000033981Gria2 0.081e+000.001e+00-2.713e-060.161e+000.485e-010.081e+00-1.161e+00
ENSMUSG00000079037Prnp 0.081e+000.161e+00-1.675e-03-0.171e+000.221e+000.141e+001.217e-01
ENSMUSG00000022961Son 0.081e+00-0.341e+00-2.456e-05-0.051e+000.544e-01-0.301e+002.003e-02
ENSMUSG00000028649Macf1 0.061e+00-0.251e+00-3.107e-060.011e+000.437e-010.151e+001.543e-01
ENSMUSG00000029838Ptn 0.041e+00-0.311e+00-1.239e-020.489e-01-0.953e-01-0.481e+003.326e-06
ENSMUSG00000059003Grin2a 0.031e+00-1.148e-01-2.526e-05-0.141e+001.362e-05-0.261e+00-1.861e+00
ENSMUSG00000004933Matk 0.011e+000.011e+00-1.722e-030.141e+000.534e-01-0.021e+00-1.471e+00
ENSMUSG00000024661Fth1 -0.001e+00-0.521e+000.188e-01-0.697e-010.844e-02-0.471e+000.371e+00
ENSMUSG00000022564Grina -0.021e+000.111e+00-3.069e-06-0.181e+000.623e-01-0.131e+001.543e-01
ENSMUSG00000028161Ppp3ca -0.031e+00-0.321e+00-2.365e-05-0.171e+000.988e-030.061e+00-1.621e+00
ENSMUSG00000097156Gm3764 -0.041e+00-0.241e+00-2.161e-030.419e-01-0.191e+00-0.521e+002.984e-05
ENSMUSG00000032482Cspg5 -0.051e+00-0.271e+00-2.445e-040.774e-01-1.332e-020.241e+002.937e-05
ENSMUSG00000057897Camk2b -0.081e+00-0.271e+00-2.407e-05-0.211e+001.148e-04-0.151e+00-1.461e+00
ENSMUSG00000026576Atp1b1 -0.101e+00-0.171e+00-1.625e-03-0.141e+000.825e-020.131e+00-0.991e+00
ENSMUSG00000004207Psap -0.111e+000.431e+00-1.441e-02-0.401e+000.121e+000.291e+001.642e-01
ENSMUSG00000053477Tcf4 -0.171e+00-0.111e+00-2.464e-050.071e+000.777e-020.081e+000.131e+00
ENSMUSG00000020524Gria1 -0.328e-01-0.801e+00-3.123e-06-1.141e-011.914e-11-0.121e+00-1.001e+00
ENSMUSG00000029309Sparcl1 -0.378e-010.211e+00-0.311e+00-0.916e-01-1.354e-020.481e+003.793e-08
ENSMUSG00000037852Cpe -0.378e-01-0.321e+000.228e-01-0.489e-010.358e-01-0.531e+002.811e-04
ENSMUSG00000005089Slc1a2 -0.437e-01-0.461e+00-0.101e+000.439e-01-0.952e-01-0.351e+003.506e-08
ENSMUSG00000026701Prdx6 -0.478e-01-0.481e+00-0.031e+00-0.461e+00-0.201e+00-0.461e+003.954e-08
ENSMUSG00000031760Mt3 -0.497e-01-0.491e+000.811e-01-1.034e-010.041e+00-0.571e+003.422e-06
ENSMUSG00000035131Brinp3 -0.595e-01-0.031e+00-3.501e-062.591e-17-3.898e-15-0.331e+00-1.581e+00
ENSMUSG00000037706Cd81 -0.665e-010.481e+00-1.802e-02-0.181e+00-0.291e+00-0.221e+003.754e-08
ENSMUSG00000022037Clu -0.955e-01-0.791e+000.307e-01-1.376e-01-1.363e-01-0.941e+005.302e-12
ENSMUSG00000031765Mt1 -1.032e-01-0.301e+001.261e-02-1.303e-01-1.023e-01-1.051e+004.506e-12
ENSMUSG00000020734Grin2c -1.346e-01-1.401e+00-1.098e-01-2.355e-01-1.556e-01-1.601e+006.741e-12
ENSMUSG00000034796Cpne7 -1.376e-03-0.231e+00-2.005e-03-2.535e-052.923e-21-0.981e+00-2.271e+00
ENSMUSG00000065947mt-Nd4l -1.404e-040.571e+002.661e-14-1.112e-01-1.317e-03-0.131e+00-0.461e+00
ENSMUSG00000026473Glul -1.462e-02-0.121e+001.658e-04-1.323e-01-1.251e-01-1.261e+004.562e-12
ENSMUSG00000020591Ntsr2 -1.517e-02-0.591e+00-2.114e-02-2.187e-021.131e-01-1.861e+005.022e-12
ENSMUSG00000005360Slc1a3 -1.529e-02-0.531e+00-0.787e-01-2.485e-02-1.045e-01-2.765e-016.302e-21
ENSMUSG00000064356mt-Atp8 -1.532e-050.611e+002.793e-13-1.451e-02-1.006e-02-0.411e+00-0.531e+00
ENSMUSG00000064367mt-Nd5 -1.532e-050.631e+002.773e-13-1.441e-02-1.113e-02-0.251e+00-0.771e+00
ENSMUSG00000007097Atp1a2 -1.556e-020.541e+00-0.806e-01-1.375e-01-1.873e-02-2.051e+005.783e-18
ENSMUSG00000031762Mt2 -1.574e-02-0.301e+001.175e-02-1.961e-01-0.628e-01-1.511e+005.044e-13
ENSMUSG00000064358mt-Co3 -1.611e-060.691e+002.783e-13-1.484e-03-1.131e-02-0.251e+00-0.831e+00
ENSMUSG00000064351mt-Co1 -1.631e-060.691e+002.813e-13-1.466e-03-1.236e-03-0.281e+00-0.591e+00
ENSMUSG00000064357mt-Atp6 -1.657e-070.691e+002.833e-13-1.562e-03-1.189e-03-0.261e+00-0.761e+00
ENSMUSG00000064370mt-Cytb -1.676e-070.721e+002.853e-13-1.582e-03-1.264e-03-0.261e+00-0.711e+00
ENSMUSG00000064341mt-Nd1 -1.704e-070.771e+002.833e-13-1.533e-03-1.236e-03-0.241e+00-1.241e+00
ENSMUSG00000017390Aldoc -1.708e-03-0.971e+001.047e-02-0.769e-01-1.421e-01-0.581e+005.084e-15
ENSMUSG00000064354mt-Co2 -1.723e-070.741e+002.863e-13-1.485e-03-1.236e-03-0.311e+00-0.931e+00
ENSMUSG00000002985Apoe -1.773e-02-0.691e+00-0.291e+00-1.733e-01-2.083e-02-1.611e+006.241e-19
ENSMUSG00000064363mt-Nd4 -1.771e-070.701e+002.893e-13-1.686e-04-1.189e-03-0.241e+00-0.481e+00
ENSMUSG00000064345mt-Nd2 -1.771e-070.711e+002.893e-13-1.706e-04-1.274e-03-0.211e+00-0.271e+00
ENSMUSG00000004558Ndrg2 -1.781e-02-0.721e+001.362e-02-1.573e-01-1.153e-01-1.651e+005.281e-15
ENSMUSG00000064360mt-Nd3 -1.969e-090.721e+003.043e-13-1.814e-04-1.324e-03-0.251e+00-0.991e+00
ENSMUSG00000004892Bcan -1.978e-04-0.561e+00-1.312e-01-1.761e-011.059e-02-1.061e+004.896e-14
ENSMUSG00000027447Cst3 -2.122e-031.209e-01-0.261e+00-1.773e-010.141e+00-1.661e+004.545e-08
ENSMUSG00000006205Htra1 -2.163e-02-0.381e+00-1.483e-01-0.901e+00-2.563e-02-1.751e+006.603e-18
ENSMUSG00000030605Mfge8 -2.479e-03-0.801e+00-0.986e-01-1.636e-01-1.882e-01-1.921e+006.871e-20
ENSMUSG00000022708Zbtb20 -2.483e-11-1.877e-02-4.448e-09-3.462e-104.282e-56-2.153e-020.651e+00
ENSMUSG00000050953Gja1 -2.624e-02-0.021e+00-0.641e+00-1.478e-01-2.491e-01-1.921e+006.832e-15
ENSMUSG00000026424Gpr37l1 -3.335e-04-0.591e+00-1.952e-01-1.119e-01-2.191e-01-2.881e+007.242e-21
ENSMUSG00000015090Ptgds -3.427e-015.701e-02-2.111e+00-3.541e+00-2.991e+00-2.691e+00-2.021e+00
ENSMUSG00000028517Plpp3 -3.453e-03-0.721e+00-0.421e+00-2.633e-01-1.654e-01-2.741e+007.206e-17
This plot shows the Sequencing Saturation metric as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. Sequencing Saturation is a measure of the observed library complexity, and approaches 1.0 (100%) when all converted mRNA transcripts have been sequenced. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point. The dotted line is drawn at a value reasonably approximating the saturation point.

Sequencing Saturation

010k20k30k40k50k00.20.40.60.81
Mean Reads per CellSequencing Saturation
 
This plot shows the Median Genes per Cell as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point.

Median Genes per Cell

010k20k30k40k50k0200400600800
Mean Reads per CellMedian Genes per Cellmm10