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 cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 6 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22.

  mus tissues liver-specific kidney bulk microarray chip-seq

• Role of p16/MTS1, cyclin D1 and RB in primary oral cancer and oral cancer cell lines.

  PMID 10389982 · PMC2363027 · British journal of cancer · 1999 · 7 claims · 5 setups

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  p16/MTS1 mutations and loss of expression are very common in OSCC cell lines and less frequent in primary OSCC tumours

  oscc same frozen pcr western extraction

• Multiple molecular marker testing (p53, C-Ki-ras, c-erbB-2) improves estimation of prognosis in potentially curative resected non-small cell lung cancer.

  PMID 10945494 · PMC2374666 · British journal of cancer · 2000 · 6 claims · 4 setups

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  Testing 3 molecular markers (c-Ki-ras, p53, c-erbB-2) together improves estimation of prognosis compared to single marker testing and defines low- and high-risk groups for treatment failure in R0-resected NSCLC.

  paired frozen nsclc sscp immunohistochemistry clinical

• Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

  PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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  277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

  umbilical ucb zebrafish microarray fluorescence-activated quantitative

• Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.

  PMID 40721291 · PMC12305944 · Life science alliance · 2025 · 8 claims · 7 setups

  Has reproduction · 74

  Acute MYC (T58I) and BCL2 overexpression drives an aberrant B-cell differentiation phenotype with altered surface marker expression while functional antibody secretion is retained

  peripheral rna-seq flow edu antibody

• Exploring microproteins from various model organisms using the mip-mining database.

  PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups

  Has reproduction · 85

  Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions

  nine cerevisiae thaliana bulk transcriptome growth

• A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

  PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 6 claims · 5 setups

  Has reproduction

  The glycosyltransferase gene AsRCOM is the most critical disease-resistance gene against agave purple curl leaf disease, and its overexpression significantly enhances resistance.

  agave a.h11648 bulk wgcna qpcr

• Transcriptional and proteomic profiling in a cellular model of DYT1 dystonia.

  PMID 19665049 · PMC2774817 · Neuroscience · 2009 · 8 claims · 7 setups

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  Accumulation of mutant torsinA(ΔE) in the nuclear envelope is not sufficient to cause transcriptional dysregulation

  pc6-3 hek293 microarray 2-dige mass

• Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

  PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  KYNU expression is decreased in melanoma despite a high KYNU mutation rate in the TCGA database

  tcga-skcm melanoma keratinocytes differential copy methylation

• Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.

  PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 8 claims · 8 setups

  Has reproduction · 73

  NF1 is highly expressed in cetuximab-sensitive CRC cell lines and minimally expressed in cetuximab-resistant ones

  crc cetuximab-sensitive sirna ffpe western growth colony

• Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression.

  PMID 14710226 · PMC2395336 · British journal of cancer · 2004 · 7 claims · 5 setups

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  There is a surprisingly high correlation between transcription and translation for the subset of genes studied by parallel microarray and proteomics analysis

  hb4a serum-starved cdna 2d-difference immunoblotting

• P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

  PMID 20046837 · PMC2798614 · PloS one · 2009 · 8 claims · 8 setups

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  p19 regulates telomerase activity through its interaction with p73α/β proteins

  yeast hela yeast facs pkc

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 75

  All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.

  haβ-ki models degs app bulk functional master

• Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein.

  PMID 16507314 · PMC7111751 · Virology · 2006 · 7 claims · 8 setups

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  Expression of SARS-CoV E protein in mammalian cells alters membrane permeability

  hela sf9 hygromycin site-directed subcellular

• 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

• Nucleotide oligomerization domain-2 interacts with 2'-5'-oligoadenylate synthetase type 2 and enhances RNase-L function in THP-1 cells.

  PMID 19853919 · PMC2787966 · Molecular immunology · 2009 · 7 claims · 6 setups

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  OAS2 is identified as a novel NOD2-binding partner in THP-1 cells by tandem affinity purification and mass spectrometry

  thp-1 hek293 tandem co-immunoprecipitation oas2

• 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

• Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia.

  PMID 32581241 · PMC7314847 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 92

  IL7R interacts/colocalizes with CXCR4 on the cell surface, recruiting BCR-ABL1 and JAK kinases into close proximity to form a platform for transformation

  bm-derived pediatric bcr-abl1-transformed nod-scid bulk gene flow

• Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

  PMID 35012625 · PMC8743438 · Genome biology · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  GENEVA is a semi-automated, study-design-agnostic framework that mines large-scale public RNA-seq data to identify conditions modulating a gene of interest's expression

  gtex lncap heart breast bulk rna-seq meta-analysis

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden