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).

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

  PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

  Has reproduction · 93

  Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

  homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic

• Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

  PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups

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  The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.

  brain exon targeted principal

• Structural evolution of the protein kinase-like superfamily.

  PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

  bank representative same kinase comparative manual structure-annotated

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

  PMID 18974839 · PMC2572839 · PloS one · 2008 · 7 claims · 6 setups

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  Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients

  ileal p16s otu pseudomonas nested cloning

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal

• Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

  PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups

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  151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations

  leukocytes leukocyte-derived archived comparison whole-genome quantitative snp

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• An enhanced single base extension technique for the analysis of complex viral populations.

  PMID 19834618 · PMC2759544 · PloS one · 2009 · 8 claims · 7 setups

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  The MDAP single base extension microarray platform measures nucleotide frequency at each genomic position in a complex population without requiring prior knowledge of candidate SNPs

  transcribed poliovirus array-bound array single oligonucleotide sbe

• Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection.

  PMID 16102740 · PMC7124242 · Clinica chimica acta; international journal of clinical chemistry · 2006 · 6 claims · 7 setups

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  The Luminex xMAP system uses spectrally distinct dyed microspheres (up to 100 sets) read by dual lasers to enable simultaneous multiplexed analysis of up to 100 reactions in one vessel.

  genomic apoe hla whole-genome direct oligonucleotide single