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 41

System / cell line: gene ✕ Assay: serial ✕ Clear

A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.

PMID 16420688 · PMC1382211 · BMC genomics · 2006 · 7 claims · 4 setups

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PBEC and KC SAGE libraries show approximately 80% overlap in expressed tags, indicating high similarity in gene repertoire

bronchial keratinocytes pbec types sage rt-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
The UCSC Genome Browser Database: 2008 update.

PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

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The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

zebrafish yale vertebrate non-human sage expression snp
A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

giardia serial northern western
Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

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Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

normal genome-wide same omim microarray sage computational
Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

PMID 19969118 · PMC2821965 · Vaccine · 2010 · 7 claims · 8 setups

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rMVA expressing multiple antigens under the mH5 promoter exhibit remarkable genetic stability and maintain potent immunogenicity after serial passage

rmva-infected individually bhk-21 pbmc qpcr western southern
Chipping away at 'stemness'.

PMID 15287966 · PMC507869 · Genome biology · 2004 · 8 claims · 6 setups

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Global gene-expression analyses across five independent studies identify known and new candidate regulators of human ES-cell growth, self-renewal, and pluripotency.

microarray sage custom
Heterogeneity of p53 mutational status in intramucosal carcinoma of the colorectum.

PMID 11223545 · PMC5926696 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 4 setups

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p53 gene mutations occur and diverge at the intramucosal carcinoma stage, before submucosal invasion

endoscopically same pcr-based immunohistochemistry histologic
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
Gene function in the mammalian genome, courtesy of the mouse.

PMID 12537544 · PMC151280 · Genome biology · 2003 · 8 claims · 8 setups

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Mosaicism of Mus musculus domesticus and Mus musculus musculus haplotypes exists across the inbred laboratory mouse genome, and genome-wide haplotype mapping can enhance positional cloning

inbred genome mice model genome-wide large-scale phenotypic
Genome Network and FANTOM3: assessing the complexity of the transcriptome.

PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

fantom3 genome large-scale mammalian cage full-length genome
Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

saliva amplified extracted differentially genome quality extraction
Tissue compartment analysis for biomarker discovery by gene expression profiling.

PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

kidney pure serial rt-pcr sage histo-morphometry
Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

PMID 19682357 · PMC2782262 · BMC microbiology · 2009 · 8 claims · 5 setups

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The RCA assay correctly identified all ERG11 mutations in eight 'reference' azole-resistant C. albicans isolates with known mutations.

clinical pcr template padlock sequencing antifungal
Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.

PMID 37311769 · PMC10264453 · Nature communications · 2023 · 7 claims · 8 setups

Has reproduction · 69

Porcine kidney xenografts transplanted into NHPs show only modest growth over time.

yucatan cynomolgus nhp parathyroid bulk serial plasma
High incidence of human bocavirus infection in children in Spain.

PMID 17904416 · PMC7108365 · Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2007 · 8 claims · 6 setups

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HBoV is a significant contributor to acute lower respiratory tract infection in young children in Spain

nasopharyngeal cloned hbov-positive urine nested multiplex sanger
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

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A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

genome affymetrix antisense mirna computational microarray sage
Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

PMID 34643182 · PMC8555986 · eLife · 2021 · 8 claims · 8 setups

Has reproduction · 84

Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm/pSHF via an evolutionarily conserved intronic enhancer.

micro-dissected dissected e9.5 xenopus bulk rt-qpcr whole-mount
Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions.

PMID 31681245 · PMC6813237 · Frontiers in microbiology · 2019 · 8 claims · 5 setups

Has reproduction · 73

S. aureus COL (MRSA) can survive and grow under acidic (pH5) and alkaline (pH9) conditions both planktonically and as a biofilm.

aureus growth microarray extraction
B lymphocyte involvement in ankylosing spondylitis: the heavy chain variable segment gene repertoire of B lymphocytes from germinal center-like foci in the synovial membrane indicates antigen selection.

PMID 11299060 · PMC30712 · Arthritis research · 2001 · 8 claims · 4 setups

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70 rearranged heavy chain VH genes from AS synovial membrane were characterized; 59 were potentially functional

frozen lymphocytes microdissected pcr double microdissection semi-nested

Experiments

A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes.

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

The UCSC Genome Browser Database: 2008 update.

A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

Chipping away at 'stemness'.

Heterogeneity of p53 mutational status in intramucosal carcinoma of the colorectum.

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

Gene function in the mammalian genome, courtesy of the mouse.

Genome Network and FANTOM3: assessing the complexity of the transcriptome.

Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

Tissue compartment analysis for biomarker discovery by gene expression profiling.

Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.

High incidence of human bocavirus infection in children in Spain.

Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions.

B lymphocyte involvement in ankylosing spondylitis: the heavy chain variable segment gene repertoire of B lymphocytes from germinal center-like foci in the synovial membrane indicates antigen selection.