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).

• TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.

  PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups

  Has reproduction · 78

  TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.

  embryonic trim28 mrna-seq trim28 h3k9me3

• DNA methylation of cancer genome.

  PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups

  Full-text index only

  Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.

  embryonic germ heterozygous cancer gene hypomorphic methyltransferase

• Gata-3 and mammary cell fate.

  PMID 17381824 · PMC1868924 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

  Full-text index only

  Gata-3 is required for formation of mammary placodes during embryonic development

  mammary gata-3 k14-cre mmtv-cre microarray lacz cre

• Monocarboxylate Transporter-2 Expression Restricts Tumor Growth in a Murine Model of Lung Cancer: A Multi-Omic Analysis.

  PMID 34638954 · PMC8508890 · International journal of molecular sciences · 2021 · 7 claims · 7 setups

  Has reproduction · 53

  Reduced MCT2 expression promotes increased tumor growth and local invasiveness in a murine TC1 lung carcinoma model

  mct2 tumor tumor-associated fecal western tumor transmission

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

  Full-text index only

  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• Identification of gene interactions associated with disease from gene expression data using synergy networks.

  PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups

  Full-text index only

  Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.

  prostate simulated microarray simulated permutation

• Geographical genomics of human leukocyte gene expression variation in southern Morocco.

  PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

  Full-text index only

  Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

  peripheral blood genotype randomly genome-wide population admixture

• The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

  PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups

  Has reproduction · 67

  A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.

  facs-isolated fcrls+ sorted app-ps1 nanostring sequencing quantitative

• Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

  PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

  Full-text index only

  Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

  neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic

• A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

  PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

  Full-text index only

  A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

  cases patients postmortem whole-genome cox linear

• DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

  PMID 41055236 · PMC12505516 · RNA biology · 2025 · 7 claims · 5 setups

  Has reproduction · 100

  DeepRNA-Reg, a recurrent neural network-based algorithm, predicts differentially enriched sites in paired HITS-CLIP datasets and outperforms dCLIP 1.7.

  dgcr8 mir-23 deeprna-reg ago2 gene flow

• DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits.

  PMID 31694669 · PMC6836538 · Genome biology · 2019 · 8 claims · 8 setups

  Has reproduction · 56

  DESE is a unified iterative framework that estimates driver tissues of complex diseases/traits from tissue-selective expression of GWAS-associated genes, and outputs prioritized susceptibility genes as a byproduct

  tissues schizophrenia bipolar coronary rna-seq gwas gene

• Functional genomics of early cortex patterning.

  PMID 16515721 · PMC1431711 · Genome biology · 2006 · 7 claims · 6 setups

  Full-text index only

  The neocortical protomap is established as continuous rostro-caudal gradients of gene expression in progenitor cells, not discrete compartments

  neocortex embryonic fgfr1-mutant cortex oligonucleotide situ microarray

• Phase transition specified by a binary code patterns the vertebrate eye cup.

  PMID 34757798 · PMC8580326 · Science advances · 2021 · 7 claims · 6 setups

  Has reproduction · 74

  FGF signaling is required for ciliary margin (CM) development; loss of FGFRs in peripheral retina abolishes CM markers and causes aniridia

  embryonic e13.5 retina immunostaining single-cell velocity

• Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

  PMID 37572656 · PMC10576612 · Immunity · 2023 · 8 claims · 8 setups

  Has reproduction · 68

  Arg1 expression is induced in lung CD4+ T cells during in vivo influenza infection, ranking among the most highly induced genes.

  flow-sorted cd3 lung cd4+ bulk flow western

• Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

  PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction

  Discovery and replication GWAS of SBP, DBP and pulse pressure in up to 776,078 individuals identified 208 novel common blood pressure SNPs and 53 rare variants.

  mvp tissues kidney gwas genome-wide transcriptome-wide

• An Erg-driven transcriptional program controls B cell lymphopoiesis.

  PMID 32541654 · PMC7296042 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 81

  Erg is essential for early B-cell development, with its loss causing developmental arrest at the pre–proB (Hardy fraction A-to-B) stage

  erg pre–prob b220+ prob lacz bulk flow

• Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

  PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 7 claims · 8 setups

  Has reproduction · 79

  Meta-analysis confirms a positive bidirectional association between DED and DEP (DED patients have increased DEP prevalence and vice versa).

  studies taiwan twb ded meta-analysis genome-wide conditional

• Identification and Mechanisms of Osteocyte Subsets Involved in the Pathological Progression of Osteoporosis.

  PMID 41250977 · PMC12850396 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Has reproduction · 57

  Six distinct osteocyte subsets (C1-C6) exist in mouse bone, identified by single-cell sequencing.

  femoral dmp1-cre+ sorted bmdms single-cell flow western

• JunB Is Critical for Survival of T Helper Cells.

  PMID 35837408 · PMC9273772 · Frontiers in immunology · 2022 · 7 claims · 7 setups

  Has reproduction · 69

  JunB is required for clonal expansion of Th1, Th2, and Th17 cells

  ot-ii junb naive th1 flow adoptive th1