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.
Alert | Value | Detail | |
Specified probe barcode ID(s) not detected | The 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
Cells | Median reads per cell | Median genes per cell | Total genes detected | Median UMI counts per cell | Confidently mapped reads in cells |
14,631 | 22,797 | 4,906 | 17,647 | 12,704 | 93.12% |
Cell Multiplexing
Physical library ID | Cells detected in this sample | Cells detected in other samples |
GEX_1 | 14,631 (40.86%) | 21,175 (59.14%) |
Mapping Metrics (Amongst Reads From Cells Assigned To Sample)
Number of reads from cells called from this sample | Reads mapped to probe set | Reads confidently mapped to probe set | Reads confidently mapped to filtered probe set |
579,024,213 | 99.31% | 98.77% | 98.43% |
UMIs from Genomic DNA
Estimated UMIs from genomic DNA | Estimated UMIs from genomic DNA per unspliced probe |
0.02% | 2 |
t-SNE Projection
Clustering Type:
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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