File size: 2,290 Bytes
70070cd | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | # Dataset: X-Atlas/Pisces
X-Atlas/Pisces is the largest CRISPRi Perturb-seq compendium to date, comprising
**25.6 million perturbed single-cell transcriptomes** across 7 biologically diverse contexts.
## Screens
| Screen | Cell Type | Perturbations | Perturbed Cells | Median KD % |
|--------|-----------|--------------|----------------|-------------|
| HCT116 | Colorectal cancer | 18,924 | 3.4M | 70% |
| HEK293T | Kidney epithelial | 18,312 | 4.5M | 48% |
| HepG2 | Hepatocellular carcinoma | 9,735 | 2.6M | 85% |
| iPSC | Induced pluripotent stem cells | 10,095 | 4.2M | 82% |
| Jurkat Resting | T lymphoblastic leukemia | 10,872 | 2.8M | 79% |
| Jurkat Active | CD3/CD28-stimulated T cells | 10,878 | 2.8M | 71% |
| iPSC Multi-Diff | Multi-lineage differentiation | 12,175 | 5.1M | 96% |
## Data Access
Test perturbation sets (held-out genes from HepG2 and iPSC, plus full Jurkat Resting/Active screens)
are available on HuggingFace:
[:hugging: Xaira-Therapeutics/X-Atlas-Pisces](https://huggingface.co/datasets/Xaira-Therapeutics/X-Atlas-Pisces){ .md-button }
## Format
Data is provided as `.h5ad` files (AnnData format) with:
- `.X` — log-normalized expression (log1p CP10k)
- `.obs["perturbation"]` — gene target of CRISPRi knockdown
- `.obs["is_control"]` — boolean flag for non-targeting controls
- `.var_names` — ENSEMBL gene IDs
## Context-Dependent Biology
A key finding from X-Atlas/Pisces is that perturbation effects are strongly context-dependent.
Hierarchical clustering of perturbation effect profiles (F1 scores from a per-perturbation
binary classifier) reveals three classes:
- **Context-independent**: core essential machinery (e.g., mitochondrial ribosome subunits,
oxidative phosphorylation) — enriched in shared metabolic functions
- **Context-specific**: lineage-defining regulators — enriched in cell-type-specific pathways
(e.g., hypoxia response in HepG2, neural crest differentiation in iPSC)
- **Conserved proximal / variable distal**: perturbations where the direct consequence is
consistent but downstream cascades diverge by context
This context-dependence motivates X-Cell's cross-attention architecture, which conditions
predictions on multi-modal biological priors rather than learning context-invariant representations.
|