Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 6

System / cell line: sequencing ✕ Assay: atac-sequencing ✕ Clear

Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

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Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

rcc internal tumor state-specific single-cell multiome copy
Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

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Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell
Oxidized LDL Induces Pro-Inflammatory Transcriptomic and Epigenomic Responses in Human CD4(+) T Cells.

PMID 41707046 · PMC12916081 · FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026 · 8 claims · 6 setups

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Ox-LDL causes a shift toward a pro-inflammatory, cytokine-producing transcriptomic state in activated CD4+ T cells

activated naïve cd4+ cad rna-sequencing atac-sequencing chip-sequencing
Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

PMID 41649260 · PMC12880807 · eLife · 2026 · 8 claims · 8 setups

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13LGS cone photoreceptors arise from both early-stage and late-stage neurogenic progenitors, unlike mice where cones arise only from early-stage progenitors

13-lined retina 13lgs retinal single-cell scrna-seq chromvar
Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.

PMID 41540108 · PMC13004696 · Nature medicine · 2026 · 7 claims · 7 setups

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GPRC5D antigenic drift/mutational events occurred in 68.4% of relapsed cases following anti-GPRC5D TCE therapy (13/19 evaluable patients)

cd138+ pbmcs cohort bulk single-cell targeted
Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.

PMID 41673768 · PMC12998334 · Journal of experimental & clinical cancer research : CR · 2026 · 6 claims · 8 setups

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Organoids derived from malignant effusions of PDAC patients reproducibly generate peritoneal metastases after orthotopic implantation into the pancreas of immunodeficient mice

pdac organoids frozen pdox orthotopic single-nucleus single-cell

Experiments

Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

Oxidized LDL Induces Pro-Inflammatory Transcriptomic and Epigenomic Responses in Human CD4(+) T Cells.

Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.

Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.