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 151

System / cell line: pcr ✕ Assay: validation ✕ Clear

Asthma investigators begin to reap the fruits of genomics.

PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

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Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

monkey models lung inbred cdna oligonucleotide northern
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

PMID 19860899 · PMC2774331 · BMC genomics · 2009 · 8 claims · 6 setups

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HaloCHIP is a functional antibody-free alternative to ChIP that uses covalent capture of HaloTag-fusion protein-DNA complexes on HaloLink resin

hela computational living halochip halochip-chip chip-chip
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

Has reproduction · 62

CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons

cask ko1 day mature bulk qrt-pcr western
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups

Has reproduction · 67

Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines

brain tumour gbm retrotransposon empty qrt-pcr
Paired-end mapping reveals extensive structural variation in the human genome.

PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

genomic na15510 stretched reference paired-end pcr array
Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

PMID 12702206 · PMC154576 · Genome biology · 2003 · 8 claims · 6 setups

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Segmental duplications comprise 3.53% (107.4/3,043.1 Mb) of the June 2002 human genome assembly

genome refseq-annotated chromosome chromosome-wide e-pcr ambsnp
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

personal genomic pcr-validated unrelated short-read pcr sanger
A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.

PMID 39108562 · PMC11301579 · Ecology and evolution · 2024 · 7 claims · 2 setups

Has reproduction · 93

624 DEGs were identified between summer (M7) and fall (M10) migratory P. flavescens, with 352 upregulated and 272 downregulated in M7 versus M10

pantala bulk qrt-pcr
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

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Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

cervical independent computational long real-time gene
Contribution of retrotransposition to developmental disorders.

PMID 31604926 · PMC6789007 · Nature communications · 2019 · 8 claims · 6 setups

Has reproduction · 79

De novo retrotransposition events cause a small but detectable fraction of severe developmental disorders, with 4 of 9 de novo MEIs deemed likely causative (~0.04%).

ddd overlapping proband ppg whole-exome processed matched
Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.

PMID 37810000 · PMC10559070 · Heliyon · 2023 · 7 claims · 7 setups

Has reproduction · 88

SEA and SEB treatment increases proliferation of AML cell lines.

aml cancer proliferation cytotoxicity transwell
Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

orthologous diverse tissues gene comparative est microarray
Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.

PMID 15907206 · PMC1156890 · BMC genomics · 2005 · 8 claims · 5 setups

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Regulation of mRNA stability accounts for as much as 50% of all measured changes in polyA mRNA levels, inferred from absence of corresponding nuclear transcription changes.

jurkat nuclear polya single
Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 30

Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

tumor each rna-seq whole-genome targeted pcr-based
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

PMID 17542650 · PMC1885280 · PLoS genetics · 2007 · 8 claims · 7 setups

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H3me3K9 and H3me3K27 mark largely mutually exclusive, distinct classes of transcription factor genes: H3me3K9 at ZNF genes, H3me3K27 at homeobox genes

ntera2 fibroblasts chip-chip chip-pcr expression
Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

PMID 19057677 · PMC2585813 · PLoS genetics · 2008 · 7 claims · 8 setups

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Genome-wide siRNA screening identified 92 novel genes that support melanin production in human melanocytes with a low false discovery rate.

mnt-1 melanocyte melanocytes genome-wide secondary quantitative
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
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.

PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups

Has reproduction · 85

Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) were identified for HCM by intersecting DEGs with MR-derived HCM-associated eQTLs.

left european merged degs bulk two-sample machine
Comparative genomics comes of age.

PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

Experiments

Asthma investigators begin to reap the fruits of genomics.

Identification of common genetic variation that modulates alternative splicing.

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

Paired-end mapping reveals extensive structural variation in the human genome.

Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.

Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

Contribution of retrotransposition to developmental disorders.

Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.

Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

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

Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.

Comparative genomics comes of age.