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).
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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
The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.
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Gene expression and isoform variation analysis using Affymetrix Exon Arrays.
PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups
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.
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3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.
PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups
3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).
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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
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
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Has reproduction · 92
Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity.
PMID 41124077 · PMC12795473 · Cell reports · 2025 · 6 claims · 5 setups
Non-DNA-contacting residues, especially in the loop between helices 2 and 3 and in wing 2, control mono- vs. bispecificity of FH domains for the FKH and FHL motifs
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Has reproduction · 51
Polyploidy and the petal transcriptome of Gossypium.
PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups
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.
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Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.
PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups
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
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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
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.
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Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.
PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups
The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines
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Has reproduction · 58
A comparative study of techniques for differential expression analysis on RNA-Seq data.
PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups
edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.
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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
Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients
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Has reproduction · 85
Colocalization and potential interactions of Endozoicomonas and chlamydiae in microbial aggregates of the coral Pocillopora acuta.
PMID 37196086 · PMC11809670 · Science advances · 2023 · 8 claims · 8 setups
CAMAs are located in the epidermis of the tentacle tips of P. acuta polyps
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High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.
PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups
Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing
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Has reproduction · 84
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.
PMID 27832824 · PMC5105290 · Genome biology · 2016 · 7 claims · 7 setups
The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade the main plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.
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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
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.