• Sample ID

    4554

  • Pipeline Version

    cellranger-7.1.0

  • Chemistry

    Fixed RNA Profiling

  • Reference Path

    /opt/references/refdata-gex-mm10-2020-A

  • Transcriptome

    mm10-2020-A

  • Probe Set Name

    Chromium Mouse Transcriptome Probe Set v1.0.1

  • Number of Genes Targeted

    19,059

  • Filter Probes

    On

Alerts

The analysis detected 1 warning.
AlertValueDetail
Specified probe barcode ID(s) not detectedThe following probe barcodes ID(s) were specified in config CSV but account for less than 0.25% of UMIs: BC002. This could result from adding a probe barcode to your config CSV when it was not actually used in the experiment.

Cells

CellsMedian reads per cellMedian genes per cellTotal genes detectedMedian UMI counts per cellConfidently mapped reads in cells
14,63122,7974,90617,64712,70493.12%

Cell Multiplexing

Physical library IDCells detected in this sampleCells detected in other samples
GEX_114,631 (40.86%)21,175 (59.14%)

Mapping Metrics (Amongst Reads From Cells Assigned To Sample)

Number of reads from cells called from this sampleReads mapped to probe setReads confidently mapped to probe setReads confidently mapped to filtered probe set
579,024,21399.31%98.77%98.43%

UMIs from Genomic DNA

Estimated UMIs from genomic DNAEstimated UMIs from genomic DNA per unspliced probe
0.02%2

t-SNE Projection

Clustering Type:  
−50050−40−2002040
20k40k60kUMI countst-SNE Projection of Cells Colored by UMI Countst-SNE1t-SNE2
−50050−40−2002040
Cluster 1Cluster 2Cluster 3Cluster 4Cluster 5Cluster 6Cluster 7Cluster 8Cluster 9Cluster 10Cluster 11Cluster 12Cluster 13Cluster 14Cluster 15Cluster 16Cluster 17Cluster 18Cluster 19Cluster 20Cluster 21Cluster 22Cluster 23t-SNE Projection of Cells by Clusteringt-SNE1t-SNE2

Top Features by Cluster (Log2 fold-change, p-value)

Feature
Cluster 1
Cluster 2
Cluster 3
Cluster 4
Cluster 5
Cluster 6
Cluster 7
Cluster 8
Cluster 9
Cluster 10
Cluster 11
Cluster 12
Cluster 13
Cluster 14
Cluster 15
Cluster 16
Cluster 17
Cluster 18
Cluster 19
Cluster 20
Cluster 21
Cluster 22
Cluster 23
ID
Name
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
L2FC
p-value
ENSMUSG00000051985
Igfn1
1.72
7e-16
0.42
5e-2
-0.59
1e+0
1.92
6e-10
-4.02
1e-11
-2.90
7e-13
-4.99
6e-4
-4.47
8e-5
-1.79
1e+0
-1.94
2e-2
-3.49
4e-9
-3.33
2e-5
-3.40
6e-7
-2.88
1e+0
-1.67
4e-1
-3.40
3e-1
-4.02
7e-24
-2.54
4e-1
-1.25
1e+0
2.16
7e-6
-4.79
8e-1
-7.45
3e-5
-3.03
1e+0
ENSMUSG00000034796
Cpne7
1.60
2e-16
-0.16
5e-1
-0.63
1e+0
0.82
2e-2
-0.88
5e-2
-1.15
4e-4
-5.08
2e-5
-5.37
5e-8
-1.50
1e+0
-1.03
1e-1
-0.19
9e-1
-2.30
6e-4
-2.92
4e-7
-2.63
1e+0
-2.39
5e-2
-3.33
2e-1
-2.05
1e-11
-3.30
9e-2
-1.89
4e-1
2.92
5e-15
-3.21
1e+0
-6.01
5e-6
-2.62
1e+0
ENSMUSG00000032586
Traip
1.28
4e-10
-0.71
4e-4
-0.83
1e+0
1.55
2e-7
-1.30
6e-3
-1.75
3e-7
-3.10
8e-3
-3.36
4e-4
-0.25
8e-1
-2.22
2e-3
1.58
5e-7
-2.42
4e-4
-2.10
2e-4
-3.11
1e+0
-1.85
2e-1
-2.63
4e-1
-2.77
1e-16
-2.04
5e-1
-1.98
4e-1
2.85
9e-14
-3.70
9e-1
-3.36
6e-3
-2.85
1e+0
ENSMUSG00000034009
Rxfp1
1.25
1e-9
0.50
9e-3
-1.10
1e+0
2.42
4e-19
-1.17
2e-2
-1.47
2e-5
-4.13
9e-4
-4.57
6e-6
-1.60
1e+0
-1.31
1e-1
-4.23
6e-14
-2.68
1e-4
-2.02
5e-4
-3.95
1e+0
-3.55
5e-3
-3.02
3e-1
-2.98
1e-18
-2.90
2e-1
-1.37
9e-1
0.94
1e-1
-3.58
1e+0
-6.75
5e-6
-2.91
1e+0
ENSMUSG00000036304
Zdhhc23
1.25
5e-10
0.50
7e-3
-0.34
1e+0
1.54
1e-7
-1.79
8e-5
-1.70
3e-7
-4.16
5e-4
-3.43
2e-4
-0.87
9e-1
0.18
8e-1
-0.29
8e-1
-1.64
2e-2
-2.52
9e-6
-2.82
1e+0
-2.29
6e-2
-1.70
7e-1
-2.95
1e-19
0.10
1e+0
-1.21
9e-1
1.53
2e-3
-2.73
1e+0
-4.16
7e-4
-2.69
1e+0
ENSMUSG00000006958
Chrd
1.21
1e-9
-0.18
4e-1
-0.78
1e+0
1.62
2e-8
-0.48
3e-1
-1.19
2e-4
-4.68
9e-5
-2.19
1e-2
-1.09
9e-1
-1.74
1e-2
0.85
2e-2
-1.86
6e-3
-2.38
2e-5
-2.13
1e+0
-0.50
1e+0
-3.25
2e-1
-2.54
6e-16
-0.99
1e+0
-1.98
4e-1
2.17
4e-7
-3.58
9e-1
-5.24
5e-5
-2.73
1e+0
ENSMUSG00000024883
Rin1
1.21
2e-9
0.26
2e-1
0.00
1e+0
1.01
2e-3
-2.84
2e-9
-2.21
7e-11
-2.62
2e-2
-3.20
4e-4
-0.29
8e-1
-0.41
8e-1
1.48
2e-6
-1.44
4e-2
-1.49
7e-3
-0.36
1e+0
-1.32
4e-1
-2.22
5e-1
-4.06
6e-31
-2.26
4e-1
-1.51
7e-1
1.95
1e-5
-3.99
7e-1
-3.53
3e-3
-3.01
1e+0
ENSMUSG00000037014
Sstr4
1.19
4e-9
0.43
2e-2
-0.23
1e+0
1.12
3e-4
-1.16
1e-2
-1.24
1e-4
-4.24
4e-4
-4.48
3e-6
-0.78
8e-1
-0.31
9e-1
0.07
1e+0
-1.69
2e-2
-1.55
5e-3
-1.88
1e+0
0.86
2e-1
-2.64
4e-1
-2.63
1e-16
-2.94
2e-1
-1.27
9e-1
1.69
3e-4
-2.46
1e+0
-7.00
8e-7
-2.28
1e+0
ENSMUSG00000039985
Sinhcaf
1.17
1e-8
-0.46
2e-2
-1.42
1e+0
1.95
3e-12
0.60
9e-2
-0.30
7e-1
-2.44
3e-2
-3.25
5e-4
-0.64
8e-1
-2.99
6e-5
-1.42
4e-3
-2.05
3e-3
-0.76
2e-1
-3.65
1e+0
-1.63
3e-1
-1.59
8e-1
-1.51
6e-7
-1.28
9e-1
-1.91
4e-1
1.73
1e-4
-3.11
1e+0
-2.91
2e-2
-2.81
1e+0
ENSMUSG00000063564
Col23a1
1.17
2e-8
-0.10
7e-1
-0.65
1e+0
1.88
7e-11
-2.49
3e-7
-1.85
1e-7
-2.42
4e-2
-1.37
2e-1
0.20
8e-1
-1.21
1e-1
-0.98
7e-2
-0.37
9e-1
-0.24
9e-1
-1.49
1e+0
2.47
2e-7
-2.33
5e-1
-3.98
5e-27
-3.11
1e-1
-1.50
8e-1
1.64
5e-4
-3.48
1e+0
-3.14
1e-2
-3.47
1e+0
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GEX Barcode Rank Plot

110010k512510251002510002510k25100k251M
CellsBackgroundBarcodesUMI counts

Median Genes per Cell

010k20k30k010002000300040005000
mm10Mean Reads per CellMedian Genes per Cell