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).

• Alternative splicing and bioinformatic analysis of human U12-type introns.

  PMID 17332017 · PMC1874599 · Nucleic acids research · 2007 · 8 claims · 6 setups

  Full-text index only

  The long, evolutionarily conserved polypyrimidine (Py) tract of the JNK2 U2-U12 hybrid intron provides the signal for default inclusion of the downstream alternative exon 6b in non-neuronal cells

  hela hek293 genome jnk2 rt-pcr minigene bioinformatic

• Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

  PMID 18922159 · PMC2614521 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

  Full-text index only

  PGRMC1 protein spots are differentially abundant between ER-negative and ER-positive breast tumors, with two of three spots more abundant in ER-negative tumors

  sections pooled mcf7 paraffin-embedded 2d-page shrimp viability

• The clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

  PMID 18718264 · PMC3835188 · The Journal of pediatrics · 2008 · 6 claims · 5 setups

  Full-text index only

  The patient carries two identical homozygous mutations (GC>AA at positions 197/198) in exon 1 of PCFT, causing a premature stop codon (C66X)

  parental rfc hela blood genomic [3h]5-methyltetrahydrofolate northern

• Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

  PMID 18757892 · PMC2553571 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  3'-most (L type) poly(A) sites are more conserved than upstream F/M type sites, while intronic (C/H type) sites are the least conserved

  consensus poly comparative transposable

• Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

  PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

  Full-text index only

  15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

  orthologues repair case-control phosphorylation cross-species database

• Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

  PMID 17130153 · PMC1702505 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  A single Y80A alanine substitution switches Tma endo V from purine-preferring to essentially C-specific mismatch cleavage, including the previously refractory C/C mismatch.

  synthetic k-ras endo pcr restriction

• Comprehensive splice-site analysis using comparative genomics.

  PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

  Full-text index only

  Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

  refseq u2-type genes comparative information phylogenetic

• LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

  PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

  schizosaccharomyces pombe rna-seq lasso lariat-specific

• Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe.

  PMID 16432256 · PMC1345699 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  A 17mer PNA spanning K-ras codons 12/13 can serve as both PCR clamp and sensor probe in a single-tube reaction, differentiating all 12 possible point mutations from wild-type by melting temperature shift

  wild-type mixture mutant serial melting real-time limit-of-detection

• CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

  PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

  Full-text index only

  CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

  cd4+ hela imr90 embryonic chip-seq computational gene

• Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

  PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

  Has reproduction · 98

  Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

  hg38 hela hek293t induced genome-wide high-throughput chip-seq

• Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

  PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

  coli flp il10 flp-holliday recombination site-specific computational

• Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

  PMID 17318599 · PMC1915625 · Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007 · 7 claims · 7 setups

  Full-text index only

  The T309V mutation shifts the CYP2D6 heme spin equilibrium toward the six-coordinate low-spin (6cLS) state, decreasing the five-coordinate high-spin (5cHS) fraction relative to wild type.

  recombinant cyp2d6 computational resonance uv-vis sds-page

• Cancer biomarker AKR1B10 and carbonyl metabolism.

  PMID 19028477 · PMC6193474 · Chemico-biological interactions · 2009 · 8 claims · 6 setups

  Full-text index only

  AKR1B10 reduces the anticancer drug daunorubicin to daunorubicinol, decreasing its chemotherapeutic effectiveness

  recombinant fenofibrate enzyme sds-page x-ray

• Bacteriophage Mu integration in yeast and mammalian genomes.

  PMID 18953026 · PMC2602771 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  In vitro-assembled Mu transpososomes, delivered by electroporation, efficiently integrate marker genes into yeast, mouse ES, human HeLa, and human ES cell genomes

  cerevisiae ab2.2 hela fes29 electroporation southern transposition

• Distribution and effects of nonsense polymorphisms in human genes.

  PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

  genome genes nonsense snps genome-wide snp codon

• Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

  PMID 18302728 · PMC2291454 · BMC medical genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Functional assays of TSC1–TSC2 complex activity can distinguish pathogenic TSC2 mutations from rare polymorphisms when multiple variants segregate in one family

  hek immunoprecipitated tsc2 peripheral coimmunoprecipitation rheb s6k-t389

• Genetic variation in PARL influences mitochondrial content.

  PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

  Full-text index only

  PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

  genomic nuclear parl pcr snp real-time

• The cotranslational cycle of the ribosome-bound Hsp70 homolog Ssb.

  PMID 41545346 · PMC12847954 · Nature communications · 2026 · 8 claims · 7 setups

  Has reproduction · 85

  Rpl25/uL23 is the primary ribosomal attachment site of Ssb, contacted via the Ssb-αD RKKR-motif (R596, K597, K603, R604) binding the Rpl25 EDD-motif (E77, D131, D134) and C-terminus.

  yeast non-translating rpl25-kkk type cryo-em ribosome ribosome-binding

• Lack of Toll-like receptor 4 and 2 polymorphisms in Korean patients with bacteremia.

  PMID 17179672 · PMC2721950 · Journal of Korean medical science · 2006 · 7 claims · 4 setups

  Full-text index only

  No TLR4 Asp299Gly or Thr399Ile polymorphisms were detected in either bacteremia patients or healthy volunteers

  peripheral pcr bacteremia pcr-rflp sequencing blood