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).

• Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

  PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

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  A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

  carcinoma derivative xenograft custom quantitative

• The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

  PMID 12036445 · PMC5927037 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 5 setups

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  SNI (elevated spontaneous point mutation rate without microsatellite instability) is present in rat mammary carcinoma cell lines and human breast cancer cell lines

  mammary same normal pcr-sscp direct quantitative

• Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

  PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

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  graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

  neuroblastoma same normal megabladder acgh bac principal

• Relative impact of nucleotide and copy number variation on gene expression phenotypes.

  PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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  SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

  lymphoblastoid same computational subset gene snp array

• Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.

  PMID 18784923 · PMC2755762 · Annals of hematology · 2009 · 6 claims · 4 setups

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  A non-radioactive, enzyme-coupled luminometric assay can quantify Ras activation as %GTP/(GTP+GDP) with high sensitivity (detects 1 fmol GTP)

  bone n=23 3t3 ras genomic

• Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

  PMID 19737971 · PMC2994259 · Molecular cancer research : MCR · 2009 · 8 claims · 8 setups

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  CLSPN is a mediator protein essential for the ATR- and CHK1-dependent checkpoint response to replicative stress or single-stranded DNA

  ebv-immortalized sporadic same caucasian genomic denaturing genotyping

• B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

  PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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  EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

  ebv-transformed cloned rt-pcr southern sequence

• Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

  PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

  Has reproduction · 87

  NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

  lines bulk single-cell housekeeping bulk pca single-sample

• Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

  PMID 10551321 · PMC5926156 · Japanese journal of cancer research : Gann · 1999 · 8 claims · 6 setups

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  6 of 10 glioma cell lines examined showed MMAC1 mutations with presumed loss of heterozygosity (LOH)

  glioma pcr northern rt-pcr sscp

• Molecular analysis of tumor suppressor genes, Rb, p53, p16INK4A, p15INK4B and p14ARF in natural killer cell neoplasms.

  PMID 11676855 · PMC5926606 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 5 setups

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  Gene amplification of p53 was detected in one nasal NK cell lymphoma

  same shifted neoplasm cases southern pcr-sscp direct

• Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways.

  PMID 16186129 · PMC1236719 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Targeted pso-TFO genomic crosslinks resolve via genetically separable pathways leading to either base substitutions or deletions.

  cho same uv41 6-tg small sequencing

• Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

  PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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  At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

  breast same selected hct116 expression methylation-specific rt-pcr

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

  PMID 12381271 · PMC134458 · BMC genetics · 2002 · 7 claims · 8 setups

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  UNC93A maps within the minimal region of allele loss on 6q27 between D6S264 and D6S149, centromeric to D6S149

  panel 293-t malignant same rt-pcr northern fluorescence

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site

• Proteomic studies of cholangiocarcinoma and hepatocellular carcinoma cell secretomes.

  PMID 20069059 · PMC2801507 · Journal of biomedicine & biotechnology · 2010 · 7 claims · 5 setups

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  The secretomes of cholangiocarcinoma (HuCCA-1) and four hepatocellular carcinoma cell lines show distinct, differing protein profiles.

  hucca-1 same conditioned paired sds-page trypan 1-de

• Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

  PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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  85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

  paired list differentially oscc 2-de gene interaction

• Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

  PMID 11429044 · PMC5926751 · Japanese journal of cancer research : Gann · 2001 · 6 claims · 3 setups

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  RAD50 (A)9 mononucleotide repeat is frequently frameshift-mutated in MSI-H colorectal cancer cell lines and primary tumors

  colorectal same pcr-based msi

• miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.

  PMID 34637468 · PMC8509996 · PloS one · 2021 · 7 claims · 6 setups

  Has reproduction · 100

  RBPs beyond Drosha/DGCR8/Dicer are involved in regulating miRNA biogenesis and explain its spatio-temporal nature

  tissues computational rbps clip-seq rna-seq srna-seq

• A global view of protein expression in human cells, tissues, and organs.

  PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

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  A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

  normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised