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).

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

  PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups

  Full-text index only

  CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.

  spleen cd45 hox11+ lc-ms rt-pcr immunofluorescence

• Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

  PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

  Has reproduction · 70

  AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

  head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr

• Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

  PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

  Full-text index only

  A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

  p53 tumor tumors computational retroviral linker-mediated flow

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.

  PMID 36450262 · PMC9792173 · Cell reports · 2022 · 7 claims · 7 setups

  Has reproduction · 50

  Following transient CD4 depletion, IL-21-producing Tfh cells do repopulate but are outnumbered by immunomodulatory CD4 T cells (Tregs, Th17), and IL-21+ frequency remains low within activated CD4 T cells.

  il-21-trfp cd44+ splenocytes chronically flow scrna-seq adoptive

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells are largely distinct, non-overlapping populations across murine and human aging tissues, with only rare double-positive cells

  young spleen brain single-cell mass velocity

• Human Proteinpedia: a unified discovery resource for proteomics research.

  PMID 18948298 · PMC2686511 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  Human Proteinpedia is a community portal using a distributed annotation system (DAS) to share both published and unpublished human proteomic data

  proteins tissues plasma expressing tandem immunohistochemistry mass

• Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

  PMID 33722289 · PMC7962346 · Genome biology · 2021 · 6 claims · 7 setups

  Has reproduction · 66

  A PE2-mediated single-base (C>G) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder but not heart or brain, mirroring HDR-mediated 3-bp substitution.

  zygotes aorta genomic aortae crispr prime quantitative

• Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

  PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups

  Full-text index only

  The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.

  c3h genomic bac multiple-tissue genetic yac direct

• MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia.

  PMID 16834459 · PMC1502153 · PLoS medicine · 2006 · 8 claims · 8 setups

  Full-text index only

  A somatic activating mutation in MPL (W515L, transmembrane domain) is present in 9% (4/45) of JAK2V617F-negative myelofibrosis (MF) patients

  granulocyte hapmap 32d balb sequencing genotyping proliferation

• Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

  PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

  proteins cdc candidate yersinia all-against-all computational cross-species

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell