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).

• Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes.

  PMID 41606598 · PMC12924361 · BMC biology · 2026 · 8 claims · 8 setups

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  Many unannotated genes and transcripts (MSTRG/UNTs) are pervasively generated and significantly differentially expressed in cancer cell lines and tissues across four tumor types (lung, liver, stomach, colon)

  cancer a549 unt bulk chip-seq computational

• Nanog mediated control of TBX3-GATA6 circuitry in primitive endoderm differentiation of mESCs.

  PMID 41629627 · PMC12979688 · EMBO reports · 2026 · 8 claims · 8 setups

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  NANOG partners with TBX3 and the PRC2 complex to maintain ESC identity by silencing PrE genes through distal enhancers

  rcnβh escs qpcr rna-seq chip-seq

• 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

• Developments in CORG: a gene-centric comparative genomics resource.

  PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

  upstream gene overlapping c-fos pairwise sequence comparative

• Transcriptome maps of general eukaryotic RNA degradation factors.

  PMID 31135339 · PMC6570525 · eLife · 2019 · 8 claims · 3 setups

  Has reproduction · 60

  Transcriptome-wide PAR-CLIP binding profiles of 30 RNA degradation factors reveal their distribution across different RNA classes.

  saccharomyces par-clip western crac

• Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

  PMID 10408842 · PMC2362327 · British journal of cancer · 1999 · 8 claims · 3 setups

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  No mutations were found in the coding region of GDNF in any of the 36 brain tumours analysed

  sporadic tumour tumour-derived pcr loss semi-quantitative

• Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

  PMID 15175115 · PMC425576 · BMC genetics · 2004 · 6 claims · 3 setups

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  The SLC22A1LS gene is paternally imprinted (i.e., only the maternal allele is expressed).

  genomic pcr cdna pcr-sscp sequencing

• Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers.

  PMID 15719063 · PMC548953 · PLoS biology · 2005 · 8 claims · 3 setups

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  Discovery-based genomics research can be integrated into an undergraduate curriculum, engaging large numbers of students in professional-quality research without compromising didactic training

  drosophila genomic flp p-element molecular

• PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

  PMID 17148480 · PMC1761432 · Nucleic acids research · 2007 · 8 claims · 3 setups

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  PReMod is a database of genome-wide predicted cis-regulatory modules (pCRMs) for the human and mouse genomes.

  genome chip-chip comparative

• Analysis of DAX1 (NR0B1) and steroidogenic factor-1 (NR5A1) in children and adults with primary adrenal failure: ten years' experience.

  PMID 16684822 · PMC1865080 · The Journal of clinical endocrinology and metabolism · 2006 · 8 claims · 3 setups

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  DAX1 mutations are a relatively frequent cause of adrenal failure in 46,XY phenotypic boys with adrenal hypoplasia

  genomic direct targeted

• Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

  PMID 17655765 · PMC1950490 · BMC medical genetics · 2007 · 8 claims · 3 setups

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  No coding mutations were found in NR2E1 or SNX3 in five patients with MMEP or related phenotypes

  patients unaffected sanger restriction

• Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

  PMID 18654614 · PMC2429969 · PLoS computational biology · 2008 · 7 claims · 3 setups

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  A dynamic programming method (implemented as web app Indelligent) can decode superimposed allelic sequences from a single mixed trace, using only the observed string of ambiguous peak calls, without a reference sequence or reverse trace.

  genomic artificial simulated direct computational comparative

• Mutation patterns of mtDNA: empirical inferences for the coding region.

  PMID 18518963 · PMC2438339 · BMC evolutionary biology · 2008 · 5 claims · 3 setups

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  Heteroplasmy was detected in 6.5% (3/46) of Azorean families analyzed, all caused by new point mutations with no insertions/deletions.

  extended-family same direct electropherogram molecular

• Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

  PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  LTR8B is a placentally-relevant cis-regulatory element (CRE), notably within the PSG array

  sghpl-4 bewo recombinant serum chip-exonuclease transient quantitative

• A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.

  PMID 30332484 · PMC6192621 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 63

  The CGCG element (consensus TCTCGCGAGA) is a novel promoter motif enriched in TATA-less CpG island-associated promoters of ribosomal protein and housekeeping genes

  k562 hek293t hek293t-derived motif gro-cap luciferase

• Human chromosome 7: DNA sequence and biology.

  PMID 12690205 · PMC2882961 · Science (New York, N.Y.) · 2003 · 6 claims · 2 setups

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  Presents the DNA sequence and annotation of the entire human chromosome 7

  chromosome genomic comparative

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative

• The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

  PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

  genome animal aligned est genome-wide comparative est

• MitoVariome: a variome database of human mitochondrial DNA.

  PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups

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  MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).

  mitochondrial korean sequence short restriction

• Proteomics data repositories.

  PMID 19795424 · PMC2908408 · Proteomics · 2009 · 5 claims · 5 setups

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  The YRC Public Data Repository (YRC PDR) provides a single unified interface disseminating multi-technology proteomics data (mass spectrometry, yeast two-hybrid, fluorescence microscopy, structure prediction) linked to protein annotations from many source databases.

  multi-organism yeast proteomes cerevisiae tandem yeast fluorescence