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 48

System / cell line: expressed ✕ Assay: rt-pcr ✕ Clear

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

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FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

chimpanzee hepg2 promoters liver quantitative western sirna
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

tissues inter-subspecies placenta genomic microarray rt-pcr sequencing
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
Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

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None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

breast quantitative fragment gene-expression
Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways.

PMID 16001973 · PMC1183194 · BMC cancer · 2005 · 6 claims · 5 setups

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The number of significantly differentially expressed probesets induced by each drug correlates with the known clinical therapeutic response rate of that drug in fibrosarcoma

ht1080 ht1080-derived oligonucleotide quantitative gene
Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

paired list differentially oscc 2-de gene interaction
Differentiation status determines the effects of IFNγ on the expression of PD-L1 and immunomodulatory genes in melanoma.

PMID 39736644 · PMC11687009 · Cell communication and signaling : CCS · 2024 · 6 claims · 8 setups

Has reproduction · 61

Dedifferentiation via MITF knockdown renders 624Mel melanoma cells hypersensitive to IFNγ, causing non-additive (synergistic) upregulation of IFNγ-induced immunoregulatory genes.

624mel yumm1.7 wild-type qpcr bulk luminex
Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

PMID 34719737 · PMC8629906 · Cellular and molecular life sciences : CMLS · 2021 · 7 claims · 8 setups

Has reproduction · 50

VAP-1 is expressed on a subset of human HSC and on bone marrow vasculature, forming a hematogenic niche.

facs-sorted sorted cd34+ bulk single-cell flow
Is a genetic defect in Fkbp6 a common cause of azoospermia in humans?

PMID 16983454 · PMC6275806 · Cellular & molecular biology letters · 2006 · 7 claims · 7 setups

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Human FKBP6 expression is restricted to the testis among 15 adult tissues examined

genomic bilateral testicular rt-pcr mutation testicular
Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

liver genomic hcv-infected agilent two-color semi-quantitative real-time
Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

PMID 16404425 · PMC2361188 · British journal of cancer · 2006 · 7 claims · 8 setups

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A G274A base substitution in hnRNP K mRNA is present in colorectal tumours and surrounding mucosa but absent from corresponding genomic DNA, indicating an RNA editing event rather than a germline polymorphism.

colorectal cdna matched thyroid rt-pcr restriction genomic
A distinct epigenetic signature at targets of a leukemia protein.

PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

32d sequence gene bioinformatic real-time
Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

bxpc-3 2-d maldi-tof-ms western
Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

PMID 18205922 · PMC2374452 · Arthritis research & therapy · 2008 · 7 claims · 4 setups

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A standardized 3D in vitro alginate bead model of chondrocytes stimulated with synovial fibroblast supernatants can be used to profile RA-related cartilage destruction genes

sv40 articular differentially antibody-based oligonucleotide real-time
Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

PMID 19943934 · PMC2794290 · BMC cancer · 2009 · 8 claims · 5 setups

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Hundreds of genes differentiate GISTs according to KIT versus PDGFRA mutation and expression status, despite no discriminative profile for clinical/pathological parameters.

frozen genomic formalin-fixed differentially microarray sequencing quantitative
B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

ebv-transformed cloned rt-pcr southern sequence
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

Has reproduction · 64

Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

heart degs dgat2 mitodegs microarray kegg protein-protein
Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

umbilical ucb zebrafish microarray fluorescence-activated quantitative
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

Experiments

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

Asthma investigators begin to reap the fruits of genomics.

Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways.

Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

Differentiation status determines the effects of IFNγ on the expression of PD-L1 and immunomodulatory genes in melanoma.

Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

Is a genetic defect in Fkbp6 a common cause of azoospermia in humans?

Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

A distinct epigenetic signature at targets of a leukemia protein.

Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.