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 114

System / cell line: cell-type-specific ✕ Clear

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 8 claims · 6 setups

Has reproduction · 59

Fourteen gene modules were consistently (Bonferroni-corrected) associated with ReHo across a discovery sample and two independent replication samples (including one non-Chinese HCP cohort).

healthy postmortem ahba neocortex resting-state microarray weighted
Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 51

Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl
Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations.

PMID 41811178 · PMC12978698 · eLife · 2026 · 8 claims · 8 setups

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Cell type-specific Bayesian and co-expression networks generated from BMSC-OB scRNA-seq data in Diversity Outbred mice can prioritize and contextualize genes underlying human BMD GWAS associations

bmsc-ob genes mesenchymal gtex scrna-seq cellect iterativewgcna
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

Has reproduction · 66

A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons

fmr1-adarcd-v5 single bioinformatic drosophila immunofluorescence western bulk
Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 8 claims · 6 setups

Has reproduction · 71

AHR-mediated lncRNA dysregulation may be a contributing mechanism in TCDD-elicited progression of steatosis to steatohepatitis with fibrosis

liver mm39 bulk single-nuclei ahr
Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating Reelin and ciliary gene regulatory networks.

PMID 41746809 · PMC13042203 · Cell reports · 2026 · 8 claims · 8 setups

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UPF2-mediated NMD is required for proper cortical lamination; conditional Upf2 deletion in radial glia disrupts layering of TBR1+/SATB2+ and CTIP2+/CUX1+ neurons.

cortex embryonic cortical neural immunofluorescence utero co-electroporation
Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

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GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

upd gsc-like wild-type scrna-seq differential gene
Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact
Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

PMID 41529688 · PMC7618834 · Cell genomics · 2026 · 8 claims · 7 setups

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Sex differences in the Drosophila central brain do not result from large-scale transcriptional reprogramming, but from selective modifications within shared developmental lineages mediated by dsx and fru.

drosophila central dsx+ dsx-gal4>mcd8 single-cell differential scenic
Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

urothelial urothelial-specific ureter hek293t single-cell poly fluorescence
Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

tissues genomic gtex hgmd long-read variant splice
ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

lines chromosome embryonic transcription chip-seq chromhmm hi-c
Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.

PMID 41637188 · PMC12932927 · Cell reports · 2026 · 8 claims · 8 setups

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Combined MPRA enhancer assays, RNA-seq (DE/ATU) analysis, and CRISPR-Cas9 engineering to dissect the function of 94 rare non-coding variants (RNVs) associated with blood traits

k-562 chrf-288-11 hl-60 thp-1 massively bulk crispr-cas9
Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility.

PMID 41638211 · PMC13091097 · Cell systems · 2026 · 8 claims · 7 setups

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A complex, intact gut microbiome is necessary for the steady-state transcriptional landscape of all major brain-resident cell types, with myelinating oligodendrocytes and immune cells showing the largest microbiome-dependent transcriptional response.

hippocampus cd11b+ intestinal brain single-nucleus bulk multiplex
Epigenetic context defines the transcriptional activity of canonical and noncanonical NF-κB signaling in pancreatic cancer.

PMID 41844578 · PMC13039881 · Cell death discovery · 2026 · 8 claims · 8 setups

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TNFα is the primary activator of canonical NF-κB signaling via RELA in PDAC

pdac patient-derived aspc-1 l3.6pl single-cell bulk multiplex
Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn
Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma.

PMID 41916296 · PMC13130669 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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Immune and stromal heterogeneity, rather than genetic variation, are primary drivers of gene expression ITH in iCCA

multi-region icca four lihv bulk hallmark single-cell
Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

PMID 41950003 · PMC13244359 · Cell reports · 2026 · 8 claims · 7 setups

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Multi-omics factor analysis (MOFA) integrating seven omics views from 1,358 ROS/MAP participants identifies cross-omics biological factors relating to AD phenotypes.

dorsolateral brain postmortem cortex h3k9ac bulk proteomics
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.

PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups

Has reproduction · 91

DeClust is a reference-profile-free deconvolution method that incorporates molecular subtyping directly into the deconvolution process, outputting cohort-level cancer subtype and stromal reference profiles rather than per-individual profiles

tcga simulated muscle-invasive ccrcc computational simulation-based deconvolution
Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups

Has reproduction · 95

Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells

kidney live blood snrna-seq snatac-seq bulk

Experiments

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations.

Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating Reelin and ciliary gene regulatory networks.

Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.

Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility.

Epigenetic context defines the transcriptional activity of canonical and noncanonical NF-κB signaling in pancreatic cancer.

Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma.

Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.

Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.