ATLAS / POST-QC DATASET
Atlas / Post-QC Dataset Statistics System › sys06
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/SP124_sys/sys06/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
42,769
Cells represented in this release
🧬
Total Genes
17,509
Genes represented in the source matrix
🔷
Cell Types
24
Annotated cell-type groups
🫀
Tissues
6
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% |
|---|---|---|---|---|---|
| T cells | 3,170 | 7.4119104959199% | — | — | — |
| B cells | 1,707 | 3.9912085856578% | — | — | — |
| Macrophages | 1,183 | 2.7660221188244% | — | — | — |
| Monocytes | 539 | 1.2602585985176% | — | — | — |
| Natural killer cells | 237 | 0.55413968060979% | — | — | — |
| Dendritic cells | 165 | 0.3857934485258% | — | — | — |
| Plasma B cells | 30 | 0.070144263368328% | — | — | — |
| Basal cells | 1,568 | 3.6662068320513% | — | — | — |
| Luminal epithelial cells | 1,390 | 3.2500175360658% | — | — | — |
| Glandular cells | 265 | 0.61960765975356% | — | — | — |
| Peritubular myoid cells | 247 | 0.57752110173256% | — | — | — |
| Surface epithelial cells | 162 | 0.37877902218897% | — | — | — |
| Sertoli cells | 52 | 0.12158338983843% | — | — | — |
| Theca cells | 6,205 | 14.508171806682% | — | — | — |
| Other stromal cells | 2,653 | 6.2030910238724% | — | — | — |
| Fibroblasts | 1,600 | 3.7410273796441% | — | — | — |
| Leydig cells | 549 | 1.2836400196404% | — | — | — |
| Granulosa cells | 216 | 0.50503869625196% | — | — | — |
| Smooth muscle cells | 1,109 | 2.5929996025158% | — | — | — |
| Spermatocytes | 13,945 | 32.605391755711% | — | — | — |
| Spermatids | 3,381 | 7.9052584816105% | — | — | — |
| Spermatozoa | 927 | 2.1674577380813% | — | — | — |
| Spermatogonia | 393 | 0.91888985012509% | — | — | — |
| Endothelial cells | 1,076 | 2.5158409128107% | — | — | — |
24 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 | Spermatocytes | 13945 | 32.6054 | Germ cells | #29B6F6 |
| celltype | Theca cells | 6205 | 14.5082 | Stromal cells | #2F4F4F |
| celltype | Spermatids | 3381 | 7.9053 | Germ cells | #EC407A |
| celltype | T cells | 3170 | 7.4119 | Immune cells | #EF5350 |
| celltype | Other stromal cells | 2653 | 6.2031 | Stromal cells | #008B8B |
| celltype | B cells | 1707 | 3.9912 | Immune cells | #2E7D32 |
| celltype | Fibroblasts | 1600 | 3.741 | Stromal cells | #26A69A |
| celltype | Basal cells | 1568 | 3.6662 | Epithelial cells | #78909C |
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