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).

• A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

  PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

  tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided

• The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.

  PMID 41978268 · PMC13076225 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Single-nucleus Hi-C reveals CTCF-independent contact domains with stable boundaries defined by convergently oriented transcription units (TUs)

  chicken computational oocytes single-nucleus nome-seq rna-seq

• Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.

  PMID 41943068 · PMC13188692 · Genome biology · 2026 · 8 claims · 6 setups

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  38,068 REs were identified in B. napus seed tissue by integrating ATAC-seq (OCRs) and BS-seq (UMRs) data from four accessions

  seed napus identified genome-wide atac-seq bisulfite hi-c

• Alexander Meissner: learning the reprogramming code.

  PMID 19704017 · PMC2733751 · The Journal of cell biology · 2009 · 8 claims · 6 setups

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  A defined set of factors present in oocytes and embryonic stem (ES) cells can reprogram a somatic cell to pluripotency, as shown by nuclear transfer and ES cell/somatic cell fusion experiments

  blastocysts somatic fused genomic nuclear inducible fusion

• Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

  PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups

  Has reproduction

  Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types

  types encode chip-seq chromhmm dnase-seq

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• A distinct epigenetic signature at targets of a leukemia protein.

  PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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  Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

  32d sequence gene bioinformatic real-time

• Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.

  PMID 41839849 · PMC12992920 · Nature communications · 2026 · 8 claims · 8 setups

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  274,682 enhancers and 25,975 promoters were characterized across 24 tissues from an adult female sheep using ChIP-seq, ATAC-seq, CAGE-seq, RRBS, WGBS, and RNA-seq.

  tissues sheep pig chip-seq atac-seq cage-seq

• Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

  PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 76

  FOXM1 and RHNO1 are head-to-head bidirectional genes regulated by a shared bidirectional promoter (F/R-BDP)

  tcga ft282 gistic expression rt-qpcr