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 61

System / cell line: fibroblasts ✕ Assay: expression ✕ Clear

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
Innate immune modulation by RNA viruses: emerging insights from functional genomics.

PMID 18654572 · PMC7097543 · Nature reviews. Immunology · 2008 · 8 claims · 7 setups

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Influenza virus signals primarily through RIG-I to induce ISG expression, while West Nile virus signals through both RIG-I and MDA5 cooperatively.

embryonic liver brain serial gene-expression computational
Host-pathogen studies in the post-genomic era.

PMID 11178231 · PMC138846 · Genome biology · 2000 · 7 claims · 7 setups

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DNA arrays have been used to study host and/or pathogen gene expression for four viruses (HCMV, HHV8, HIV-1, HPV31) and two bacteria (Listeria monocytogenes, Salmonella)

foreskin b-cell t-cell normal pathogen host
Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

PMID 18654835 · PMC4973579 · Biogerontology · 2009 · 8 claims · 7 setups

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Treatment of HCA3 human diploid fibroblasts with a mild dose of H2O2 (600 μM) induces premature senescence without killing the cells.

hca3 differentially mudpit cdna semi-quantitative
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

Has reproduction · 59

Short-term stress and long-term adaptations share common metabolic pathways

great embryonic gef mapk1 bulk gene transcription
Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups

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125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells

ag09319 gm05388 nhfk whole-genome quantitative dna-associated
A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

PMID 19911041 · PMC2766639 · PLoS genetics · 2009 · 8 claims · 7 setups

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Padlock probes combined with high-throughput sequencing enable accurate, quantitative, low-bias digital RNA allelotyping of allele-specific expression

genomic pgp1 skin fibroblasts padlock quantitative gene
Novel insights into adipogenesis from omics data.

PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based
Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

PMID 18704688 · PMC2597685 · Reviews in endocrine & metabolic disorders · 2008 · 8 claims · 8 setups

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Genetic predisposition determines susceptibility and rate of progression to ESRD in diabetic patients, in addition to environmental factors

kidney proximal pbmcs macrophages gene qrt-pcr immunohistochemistry
Genomics in space life sciences.

PMID 18558380 · PMC5054090 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 6 setups

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Sudden changes in gravity alter mRNA levels of various genes, indicating molecular-level effects of microgravity

keratinocyte wi-38 candida rice microarray suppression pathogenicity
Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma.

PMID 33420019 · PMC7794422 · Nature communications · 2021 · 8 claims · 8 setups

Has reproduction · 50

SNAI2 is highly expressed in FN-RMS tumors and cell lines compared to normal tissue

rms fn-rms fp-rms imr90 rna-seq western immunohistochemistry
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

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Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

mda-mb231 epithelial breast early-stage cdna quantitative facs
Use of functional genomics to understand influenza-host interactions.

PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

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Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

hela a549 lung texas cdna microarray infection
Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

breast early-stage diffuse dlbcl gene
Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

PMID 18637129 · PMC2605190 · Experimental dermatology · 2009 · 8 claims · 5 setups

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Strict, rigorous sun protection starting at age 2 resulted in minimal skin disease (only mild lip freckling, no skin cancer) in XP2GO despite an XP diagnosis

fibroblasts xp2go post-uv host real-time
Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

PMID 18560825 · PMC2493868 · Immunogenetics · 2008 · 8 claims · 8 setups

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Neither transcriptional profiling alone nor genetic linkage analysis alone has been an effective approach to identify genes or gene networks that specify stemness or initiate differentiation/lineage specification.

escs fibroblasts hematopoietic bxd transcriptional forced long-term
A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

PMID 20003495 · PMC2802351 · Orphanet journal of rare diseases · 2009 · 8 claims · 7 setups

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A novel FAH gene mutation, c.103G>A (Ala35Thr), causes a mild, atypical form of tyrosinemia type I

fibroblasts liver genomic tnt northern western liver
Improvements to cardiovascular gene ontology.

PMID 19046747 · PMC2706316 · Atherosclerosis · 2009 · 8 claims · 8 setups

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Gene Ontology (GO) provides a controlled vocabulary that links current functional knowledge of genes to high-throughput genomic and proteomic datasets, aiding data interpretation.

coronary phospholamban mammalian lines gene expression large-scale
Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

Has reproduction · 93

An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

hff mrc5 chip-qpcr rt-qpcr chipseq
Using DNA microarrays to study host-microbe interactions.

PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene

Experiments

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

Innate immune modulation by RNA viruses: emerging insights from functional genomics.

Host-pathogen studies in the post-genomic era.

Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

Novel insights into adipogenesis from omics data.

Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

Genomics in space life sciences.

Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma.

Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

Use of functional genomics to understand influenza-host interactions.

Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

Improvements to cardiovascular gene ontology.

Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

Using DNA microarrays to study host-microbe interactions.