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).

Publications 1.3k Datasets 392.5k Experiments 19

System / cell line: map ✕ Assay: reference ✕ Clear

Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species.

PMID 18366709 · PMC2323391 · BMC genomics · 2008 · 8 claims · 5 setups

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Genome diversity among M. avium subspecies is mediated by large sequence polymorphisms (LSPs) commonly associated with mobile genetic elements.

avium microarray map selected microarray blastn sequencing
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups

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Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).

kegg 8192x8192 user-submitted species pathway zoomable sequence
A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.

lines random gene-expression connectivity
Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

PMID 16478714 · PMC1368655 · Nucleic acids research · 2006 · 7 claims · 6 setups

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SNP-MaP allele frequency estimates from pooled DNA on the 100K microarray set correlate strongly with allele frequencies from individual genotyping

pooled single same caucasian snp individual quantification
Short tandem repeats in human exons: a target for disease mutations.

PMID 18789129 · PMC2543027 · BMC genomics · 2008 · 8 claims · 6 setups

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STRs are present in exons of 92% of known human genes, unlike longer tandem repeats which are rare in exons

reference genome genes genome-wide indel disease
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission
Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups

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Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.

case hapmap snp individual allele
Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

PMID 37081150 · PMC10154250 · Nature immunology · 2023 · 8 claims · 6 setups

Has reproduction · 37

Orthogonal engineering of CD8+ T cells to co-secrete IL-2v and IL-33 (with PD-1 decoy) drives a novel synthetic effector state (C5 T_SE) that deviates from canonical PD-1+TOX+ exhaustion.

ot1 b16-ova facs-sorted engineered adoptive flow single-cell
Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

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MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

mip diagnostic is900-specific pgg
Skittle: a 2-dimensional genome visualization tool.

PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales

chromosome random alpha genome nucleotide repeat alignment
Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.

PMID 32111840 · PMC7048732 · Nature communications · 2020 · 6 claims · 8 setups

Has reproduction · 95

SuSr-D1 encodes Med15b.D, a subunit of the conserved Mediator complex that regulates transcription of protein-coding genes.

wheat cth chromosome ns1 stem adult-plant flow-sorted
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups

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CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing

treponema pcr-amplified ss14 pcr comparative dideoxy-terminator genome
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

Has reproduction · 84

Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

organisms arrayexpress-derived pride rna-sequencing single-channel two-colour
Vector algebra in the analysis of genome-wide expression data.

PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups

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The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.

saccharomyces microarray
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 38

A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

gossypium uppermost root reads bulk leaf rt-qpcr
WebGestalt: an integrated system for exploring gene sets in various biological contexts.

PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

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WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

genes gene est-based enrichment kegg
Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

normalized rainbow salmonids microsatellite sanger pcr
Nucleosome regulatory dynamics in response to TGFβ.

PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

Has reproduction · 59

SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

hepatocellular hepg2 130-bp mnase strand-specific taqman
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species.

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

Short tandem repeats in human exons: a target for disease mutations.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

Skittle: a 2-dimensional genome visualization tool.

Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.

Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Vector algebra in the analysis of genome-wide expression data.

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

WebGestalt: an integrated system for exploring gene sets in various biological contexts.

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

Nucleosome regulatory dynamics in response to TGFβ.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.