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).

• Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium.

  PMID 17407598 · PMC1852558 · BMC genomics · 2007 · 8 claims · 7 setups

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  Global protein expression profiles of cultured intestinal epithelial cell lines differ from those of intestinal epithelial scrapings in vivo

  caco-2 ht-29 hep muscle 2-d 2-de principal

• Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

  PMID 17052347 · PMC1622754 · BMC infectious diseases · 2006 · 8 claims · 4 setups

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  TMA/IHC staining patterns of GroEL, GroES, GspD, Ndk and Pyk in cell pellets generally corresponded to differential regulation patterns previously found by 2D gel proteomic analysis of IFN-γ-induced persistence

  hep-2 archival pneumoniae immunohistochemistry western gel

• Protocol for single-cell optimization objective and trade-off inference.

  PMID 41790544 · PMC12992945 · STAR protocols · 2026 · 6 claims · 6 setups

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  SCOOTI is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs

  mcf10a serum-starved contact-inhibited zygote bulk scrna-seq genome-scale

• YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.

  PMID 41533786 · PMC12802833 · Science advances · 2026 · 8 claims · 8 setups

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  TAZ represses PPARγ-bound target enhancers, evidenced by markedly reduced H3K27ac occupancy, leading to transcriptional repression of adipogenic genes including Pparg2

  c3h10t1 inguinal iwat adipose atac-seq rna-seq immunoblot

• Quemliclustat and chemotherapy with or without zimberelimab in metastatic pancreatic adenocarcinoma: a randomized phase 1 trial.

  PMID 41912809 · PMC13099643 · Nature medicine · 2026 · 7 claims · 8 setups

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  Quemliclustat combined with gemcitabine/nab-paclitaxel (G/nP) with or without zimberelimab has a safety profile consistent with G/nP alone across dose-escalation and dose-expansion phases

  mia hct-116 patients randomized rna-seq rt-pcr phase

• TBP regulates transposable element expression in early mouse embryos.

  PMID 41862641 · PMC13144441 · The EMBO journal · 2026 · 8 claims · 6 setups

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  The general transcription factor TBP binds and activates MaLR transposable elements in mouse embryos

  single embryos computational embryonic rna-seq atac-seq motif

• E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

  PMID 40716058 · PMC12318280 · STAR protocols · 2025 · 6 claims · 3 setups

  Has reproduction · 62

  E3RC is a computational framework for identifying and quantifying eRNAs and characterizing their expression and transcriptional regulation using conventional RNA-seq data.

  preimplantation genome erna bulk computational motif

• SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven two-cell totipotency transcriptional program in the mouse embryo.

  PMID 41697236 · PMC12908936 · eLife · 2026 · 8 claims · 5 setups

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  Maternal SETDB1 is required for mouse preimplantation development beyond the eight-cell stage

  2-cell single-embryo degs embryo single-embryo principal

• Topography-aware optimal transport for alignment of spatial omics data.

  PMID 41916307 · PMC13107060 · Cell reports methods · 2026 · 7 claims · 4 setups

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  TOAST extends the classical FGW objective by adding a spatial coherence term and a neighborhood consistency term to model local spatial organization and molecular heterogeneity.

  simulated dorsolateral simulated multislice ablation

• The reprogramming and function of H4K20me1 during early embryo development.

  PMID 42020515 · PMC13261155 · EMBO reports · 2026 · 7 claims · 8 setups

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  Low-input CUT&RUN (as few as 100 cells) reliably maps H4K20me1 and correlates strongly with conventional ChIP-seq

  k562 oocytes embryos zebrafish cut&run chip-seq immunofluorescence

• Integration of cytogenetic landmarks into the draft sequence of the human genome.

  PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

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  7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

  large-insert bac ml-2 dgap012 fluorescence sts array

• Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

  PMID 14970870 · PMC3215949 · British journal of cancer · 2004 · 8 claims · 7 setups

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  Nuclear β-catenin expression in GEJ adenocarcinoma cell lines correlates with enhanced TCF-mediated reporter gene transcription

  gej paired showing tumours tcf pcr-sscp bidirectional

• The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos.

  PMID 41917015 · PMC13201599 · Nature communications · 2026 · 8 claims · 8 setups

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  eccDNA is widespread in mouse preimplantation embryos across all six developmental stages examined

  ivf-derived 2-cell preimplantation fibroblasts mda-based reverse chip-seq

• ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression.

  PMID 41688464 · PMC13018553 · Nature communications · 2026 · 8 claims · 8 setups

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  ATRX deficiency downregulates α-globin (HBM/HBA) selectively in a subset of cells that exhibit DNA damage, rather than uniformly across the population

  cd34+ single day hudep-2 crispr-cas9 cfu single-cell