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).

• Predicting the effect of CRISPR-Cas9-based epigenome editing.

  PMID 41524535 · PMC12795505 · eLife · 2026 · 8 claims · 6 setups

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  Machine learning (CNN and ridge regression) models trained on histone PTM ChIP-seq and RNA-seq data from 13 ENCODE cell types accurately predict endogenous gene expression, with transcriptome-wide correlations of ~0.70-0.79 for most cell types

  hek293t k562 computational chip-seq rna-seq mnase-seq

• Temporal constraints on enhancer usage shape the regulation of limb gene transcription.

  PMID 41526337 · PMC12795824 · Nature communications · 2026 · 8 claims · 6 setups

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  Putative enhancer repertoires at limb developmental gene loci shift over time, with distinct early-acting, common-acting, and late-acting enhancers.

  limb shox2 h3k27ac transgenic bulk

• Single-cell and spatial transcriptomic profiling of cardiac fibroblasts following myocardial infarction.

  PMID 41526391 · PMC12890913 · Scientific data · 2026 · 7 claims · 6 setups

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  Cthrc1+ Reparative Cardiac Fibroblasts (RCFs) are the primary driver of the cardiac healing process after myocardial infarction

  col1α1-gfp+ heart frozen bulk single-cell spatial

• 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

• Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy.

  PMID 41530481 · PMC12877007 · Scientific reports · 2026 · 7 claims · 8 setups

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  71 genes show concordant (same-direction) expression changes and 94 genes show concordant methylation changes across both the kindling and kainic acid epilepsy models

  hippocampus sequencing reduced-representation rt-pcr

• PID1 regulates insulin-dependent glucose uptake by controlling intracellular sorting of GLUT4-storage vesicles.

  PMID 30904610 · PMC6624118 · Biochimica et biophysica acta. Molecular basis of disease · 2019 · 8 claims · 8 setups

  Has reproduction

  PID1 serves as an insulin-regulated retention adaptor protein controlling co-translocation of LRP1 and GLUT4 to the adipocyte plasma membrane

  brown bat muscle qrt-pcr western insulin

• Genomic studies of mood disorders -- the brain as a muscle?

  PMID 15833130 · PMC1088952 · Genome biology · 2005 · 7 claims · 5 setups

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  FGF family members and receptors (notably FGF1, FGF2, FGFR2, FGFR3) are down-regulated in postmortem prefrontal cortex of subjects with major depressive disorder but not in bipolar or control subjects.

  postmortem brain rodent hippocampus affymetrix quantification gene

• Systems biology of gene regulation fulfills its promise.

  PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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  Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

  unspecified embryonic five yeast chip-chip chip-pet computational

• GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

  PMID 35501696 · PMC9063052 · BMC bioinformatics · 2022 · 6 claims · 3 setups

  Has reproduction · 67

  GEMmaker, an nf-core compliant Nextflow workflow, can quantify gene expression from small to massive RNA-seq datasets while remaining reproducible via versioned containerized software.

  oryza arabidopsis generic rna-seq workflow

• Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

  PMID 12962547 · PMC212256 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  RMA-generated gene expression values are markedly less variable and more reliable than MAS5.0- and MBEI-derived values

  postmortem oligonucleotide real-time quality

• Recent additions and improvements to the Onto-Tools.

  PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups

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  The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.

  homo example mus functional pathway cross-database

• Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

  PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

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  A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

  carcinoma derivative xenograft custom quantitative

• The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

  PMID 15661077 · PMC548512 · Respiratory research · 2005 · 6 claims · 3 setups

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  IL-13 and IL-13R130Q modulate the same set of genes in human airway smooth muscle cells (HASMC)

  airway hasmc cdna taqman flow

• Operon information improves gene expression estimation for cDNA microarrays.

  PMID 16630355 · PMC1513396 · BMC genomics · 2006 · 7 claims · 3 setups

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  A hierarchical Bayesian model that borrows expression information from other genes within the same operon improves estimation of relative transcript levels.

  simulated coli simulated cdna two-color

• Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.

  PMID 41365655 · PMC12758391 · Genome research · 2026 · 8 claims · 3 setups

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  A factor-agnostic MNase-seq chromatin occupancy profiling (COP) approach can simultaneously capture genome-wide TF and nucleosome occupancy at near-nucleotide resolution from a single assay

  saccharomyces cerevisiae mnase-seq gene

• Toxicogenomics: an emerging discipline.

  PMID 12460812 · PMC1241126 · Environmental health perspectives · 2002 · 8 claims · 6 setups

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  Toxicogenomics applies genomic tools (microarrays, proteomics, metabolomics) to characterize how cells and organisms respond to chemical/drug exposures.

  drug stated acetaminophen tissues microarray gene genomic

• Viewing RNA-seq data on the entire human genome.

  PMID 28979763 · PMC5605993 · F1000Research · 2017 · 8 claims · 3 setups

  Has reproduction · 50

  RNA-Seq Viewer is a web application that visualizes genome-wide RNA-seq expression data pulled from NCBI's SRA and GEO databases using Ideogram.js

  sra web gzip-compressed rna-seq client-side network

• Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

  PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

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  Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

  alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic

• Easy and efficient ensemble gene set testing with EGSEA.

  PMID 29333246 · PMC5747338 · F1000Research · 2017 · 8 claims · 2 setups

  Has reproduction · 97

  EGSEA combines results from up to 12 prominent gene set testing algorithms to obtain a consensus ranking of biologically relevant gene sets

  mammary bulk microarray

• Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

  PMID 15099405 · PMC411067 · BMC bioinformatics · 2004 · 7 claims · 2 setups

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  Two-way ANOVA and Mack-Skillings tests on probe-level data with FDR control are substantially more powerful than t-test/Wilcoxon on probe-set level data for detecting differential expression

  fibroblast background high-density