ATLAS / POST-QC DATASET
Atlas / Post-QC Dataset Statistics System › sys08
Validated descriptive statistics for cells already present in this atlas release; this is not a report of pre-filtering QC decisions.
๐ analysis_results_v2/SP121_sys/sys08/releases/r20260808-v4/modules/stats
Scope: post_qc_descriptive / Source: validated immutable release
Limitations: Per-cell raw-count QC metrics were not exported in the v3 source release. / Statistics describe the selected post-QC cell universe; no pre/post filtering comparison is inferred.
๐ Overview
๐ QC Metrics
๐บ๏ธ UMAP
๐งฉ Composition
๐งฌ Markers
๐ Gene Stats
๐ Data 2
📋
Atlas / Post-QC OverviewDescriptive statistics for retained atlas cells; filtering metrics may be unavailable
🔬
Total Cells
62,054
Cells represented in this release
🧬
Total Genes
19,739
Genes represented in the source matrix
🔷
Cell Types
32
Annotated cell-type groups
🫀
Tissues
3
Annotated tissue groups
📦
Samples
N/A
Not exported by the post-QC descriptive statistics pipeline.
📊
Clusters
N/A
Not exported by the post-QC descriptive statistics pipeline.
📊
Median Genes/Cell
N/A
Not exported by the post-QC descriptive statistics pipeline.
📈
Median Counts/Cell
N/A
Not exported by the post-QC descriptive statistics pipeline.
⚡
Mito %
N/A
Not exported by the post-QC descriptive statistics pipeline.
🧪
Ribo %
N/A
Not exported by the post-QC descriptive statistics pipeline.
✅
Cells Passing
N/A
Validated Raw Count Thresholds Not Available.
🚫
Cells Filtered
N/A
Validated Raw Count Thresholds Not Available.
✅
Pass Rate
N/A
Validated Raw Count Thresholds Not Available.
QC filtering metrics: N/A
Validated Raw Count Thresholds Not Available. This release describes cells after upstream QC; it does not reconstruct filtering thresholds or removed-cell counts.
๐ท Cell Type / Cluster Breakdown
| Name | Cells | % | Med Genes | Med Counts | Med Mito% |
|---|---|---|---|---|---|
| Macrophages | 2,168 | 3.4937312663164% | — | — | — |
| T cells | 1,697 | 2.7347149257099% | — | — | — |
| Natural killer cells | 388 | 0.62526186869501% | — | — | — |
| Neutrophils | 174 | 0.2804009411158% | — | — | — |
| Erythroid cells | 123 | 0.19821445837496% | — | — | — |
| Granulocytes | 88 | 0.14181197021949% | — | — | — |
| B cells | 42 | 0.067682985786573% | — | — | — |
| Mast cells | 37 | 0.059625487478648% | — | — | — |
| Basophils | 11 | 0.017726496277436% | — | — | — |
| Natural killer T cells | 8 | 0.012891997292681% | — | — | — |
| Monocytes | 3 | 0.0048344989847552% | — | — | — |
| Plasma B cells | 1 | 0.0016114996615851% | — | — | — |
| Progenitor-like epithelial cells | 49 | 0.078963483417668% | — | — | — |
| Mesenchymal cells | 21,836 | 35.188706610372% | — | — | — |
| Homeostatic chondrocytes | 4,518 | 7.2807554710414% | — | — | — |
| Precursor fibrocartilage chondrocytes | 2,584 | 4.1641151255358% | — | — | — |
| Pericytes | 2,421 | 3.9014406806975% | — | — | — |
| Effector chondrocytes | 2,284 | 3.6806652270603% | — | — | — |
| Regulatory chondrocytes | 1,992 | 3.2101073258775% | — | — | — |
| Pre-hypertrophic chondrocytes | 1,476 | 2.3785735004996% | — | — | — |
| Hypertrophic chondrocytes | 1,363 | 2.1964740387405% | — | — | — |
| Proliferative chondrocytes | 963 | 1.5518741741064% | — | — | — |
| Reparative chondrocytes | 914 | 1.4729106906888% | — | — | — |
| Tendon cells | 334 | 0.53824088696941% | — | — | — |
| Fibrocartilage chondrocytes | 300 | 0.48344989847552% | — | — | — |
| Inflammatory chondrocytes | 70 | 0.11280497631095% | — | — | — |
| Pre-inflammatory chondrocytes | 26 | 0.041898991201212% | — | — | — |
| Satellite cells | 7,715 | 12.432719889129% | — | — | — |
| Type II myonuclei | 398 | 0.64137686531086% | — | — | — |
| Smooth muscle cells | 336 | 0.54146388629258% | — | — | — |
| Type I myonuclei | 126 | 0.20304895735972% | — | — | — |
| Endothelial cells | 7,609 | 12.261900925001% | — | — | — |
32 groups
๐
QC MetricsInteractive boxplots and scatter plots
๐ Distribution Summary
| Metric | Min | Q1 | Median | Mean | Q3 | Max | Std |
|---|
๐ป Genes/Cell BOXPLOT
๐ป Counts/Cell BOXPLOT
๐ป Mito % BOXPLOT
๐ป Ribo % BOXPLOT
๐ฌ Genes vs Counts SCATTER
๐บ๏ธ
UMAP EmbeddingInteractive 2D projection colored by cell type / cluster
๐บ๏ธ UMAP by Group INTERACTIVE
๐งฉ
Cell CompositionCell type proportions overall and per sample
๐ฅง Overall PIE
๐ Per-sample STACKED BAR
๐งฌ
Marker GenesTop markers per cluster and expression heatmap
๐ฅ Expression Heatmap Z-SCORE
๐
Gene StatisticsTop expressed genes and detection rates
Limited gene-statistics scope: mapped longevity genes only
Descriptive source-X expression summaries for mapped longevity genes only; this is not a whole-transcriptome top-gene analysis. Rankings and percentages on this tab are restricted to the mapped longevity panel and must not be interpreted as genome-wide top-expression results.
๐ Top Expressed BAR
๐
Data FilesDownload QC data tables
๐ Available Files
| File | Description | Action |
|---|---|---|
| composition.csv | Composition | ๐ฅ Download |
| gene_stats.csv | Gene Stats | ๐ฅ Download |
๐ Preview: composition.csv
๐ฅ Full CSV| grouping | group | count | pct | category | color |
|---|---|---|---|---|---|
| celltype | Mesenchymal cells | 21836 | 35.1887 | Stromal cells | #556B2F |
| celltype | Satellite cells | 7715 | 12.4327 | Muscle cells | #CD853F |
| celltype | Endothelial cells | 7609 | 12.2619 | Endothelial cells | #00FFFF |
| celltype | Homeostatic chondrocytes | 4518 | 7.2808 | Stromal cells | #7FFF00 |
| celltype | Precursor fibrocartilage chondrocytes | 2584 | 4.1641 | Stromal cells | #F0E68C |
| celltype | Pericytes | 2421 | 3.9014 | Stromal cells | #6B8E23 |
| celltype | Effector chondrocytes | 2284 | 3.6807 | Stromal cells | #3CB371 |
| celltype | Macrophages | 2168 | 3.4937 | Immune cells | #E9967A |
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