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).

• Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.

  PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 7 claims · 7 setups

  Has reproduction · 50

  sctRNA-seq datasets (particularly LCM-seq) show measurable off-target mRNA contamination from surrounding cell types

  brain neocortex cortex allen lcm-seq scrna-seq marker

• Charting and probing the activity of ADARs in human development and cell-fate specification.

  PMID 39537590 · PMC11561244 · Nature communications · 2024 · 8 claims · 6 setups

  Has reproduction · 100

  RNA editing (AEI) and ADAR/ADARB1/ADARB2 expression show organ-specific dynamic shifts across fetal-to-adult developmental stages in human forebrain, hindbrain, heart, liver, kidney, and testis

  organ same 8-week-old week alu site-specific gene

• 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

• 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

• 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

• 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

• 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

• Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

  PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

  Has reproduction · 84

  Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

  elegans short-read whole-animal rt-pcr

• FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

  PMID 34909283 · PMC8641482 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 75

  The FEM algorithm converts a single-cell gene expression matrix into a functional expression matrix using multi-module gene set enrichment analysis, utilizing information from all expressed genes rather than discarding filtered genes.

  pbmc pancreas liver scrna-seq single-cell fisher's dimensionality

• 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

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

  PMID 41683713 · PMC12898442 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Full-text index only

  TE expression is significantly higher in PBMCs from viral infection cohorts (and recovered individuals) compared to healthy controls

  pbmcs pbmc cd8+ single-cell cell-type expression

• Comprehensive analysis for the role of macrophage-driven genes in abdominal aortic aneurysm.

  PMID 41815567 · PMC12973086 · Cardiovascular diagnosis and therapy · 2026 · 8 claims · 8 setups

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  SMU1 is identified as a novel macrophage-related gene associated with AAA development, serving as a potential diagnostic biomarker and therapeutic target

  aaa macrophage-related merged gwas single-cell bulk rt-qpcr

• Deconvolving cell-type-specific gene expression profiles from bulk RNA-seq samples.

  PMID 41886524 · PMC13038110 · PLoS computational biology · 2026 · 8 claims · 6 setups

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  BLUE, a U-Net-based deep learning model with dual branches (U-Net for GEPs, MLP for proportions), accurately predicts cell-type proportions and cell-type-specific gene expression profiles from bulk RNA-seq.

  pbmc pancreatic aml scrna-seq-derived real scrna-seq

• 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

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 4 setups

  Has reproduction · 67

  Removal of batch effects in reference scRNA-seq datasets (via Harmony-Symphony) benefits the task of cell composition deconvolution

  pbmc derived tcga-lihc scrna-seq simulated bulk

• CellMap: precision mapping of cellular landscape in spatial transcriptomics.

  PMID 41505103 · PMC12781899 · Nucleic acids research · 2026 · 7 claims · 3 setups

  Full-text index only

  CellMap combines co-linearity of seed genes, a random forest model, and the linear assignment algorithm to achieve optimal assignment of single cells to spatial spots

  platforms single-cell expression computational scrna-seq spatial

• Mouse placentae generated by in vitro fertilization exhibit altered gene expression, activated hypoxia responses, and reduced fitness†.

  PMID 40874534 · PMC12808545 · Biology of reproduction · 2026 · 6 claims · 6 setups

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  IVF-conceived mouse placentae exhibit global and cell type–specific gene expression differences compared to FB placentae

  e12.5 differentially trophoblast placenta single-nucleus pseudobulk pathway