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 153

System / cell line: gene-expression ✕ Assay: relative ✕ Clear

Translation of genomics research at the bedside: the promise and the challenge.

PMID 18804420 · PMC2602964 · Clinical immunology (Orlando, Fla.) · 2008 · 7 claims · 4 setups

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Kodama et al. used gene expression microarrays to profile molecular perturbations in lymph nodes, spleen, and peripheral blood of NOD mice during development of type 1 diabetes

nod nod.b10 gene
Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.

PMID 32959884 · PMC7689298 · Human molecular genetics · 2020 · 8 claims · 8 setups

Has reproduction · 67

Trem2 R47H knock-in mice show gene dose-dependent decreased Trem2 expression in hippocampus, largely due to altered splicing

hippocampal microglia conditioned rt-qpcr immunohistochemistry glial
Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

PMID 18477650 · PMC2443277 · Carcinogenesis · 2008 · 8 claims · 7 setups

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HBx C-terminal deletion mutants (HBx3'-30 and HBx3'-40) produce differentially expressed gene and protein profiles in transfected Huh7 HCC cells, mostly involving transcriptional regulation, oncogenes/tumor suppressors, cell junctions, signal transduction, metabolism and immune response

huh7 frozen hcc genomic cdna two-dimensional western
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

lms independent soft gene array immunohistochemistry
Abnormalities of the p53 MDM2 and DCC genes in human leiomyosarcomas.

PMID 8198970 · PMC1969417 · British journal of cancer · 1994 · 6 claims · 8 setups

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A significant minority of leiomyosarcomas harbor p53 gene point mutations or deletions

leiomyosarcomas frozen leiomyosarcoma sarcoma sscp direct immunohistochemistry
Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

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Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic
DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

PMID 41055236 · PMC12505516 · RNA biology · 2025 · 8 claims · 5 setups

Has reproduction · 100

DeepRNA-Reg, a recurrent neural network-based algorithm, provides a superior prediction set for differential HITS-CLIP analysis compared to dCLIP.

dgcr8 mir-23 predicted ago2 gene flow
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups

Has reproduction · 80

928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase

burkholderia pseudomallei bulk tmt-based rt-qpcr
Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

hela protein-free dual-luciferase reporter thermodynamic
Adaptive history of single copy genes highly expressed in the term human placenta.

PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

term single same lists microarray comparative site
Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

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Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

hela liver gene peripheral retroviral transposon hydrodynamic
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
Recurring mutations found by sequencing an acute myeloid leukemia genome.

PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

aml-m1 tumor bone additional whole-genome snp gene-expression
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

Has reproduction · 54

In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

analysis microarray rna-seq quantitative
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
Molecular tumor profiling: translating genomic insights into clinical advances.

PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

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Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

breast ovarian panel tumor gene-expression candidate-gene large-scale
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
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

Has reproduction · 62

H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.

hymenophyllum dark-adapted annotated differentially bulk relative chlorophyll

Experiments

Translation of genomics research at the bedside: the promise and the challenge.

Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.

Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Abnormalities of the p53 MDM2 and DCC genes in human leiomyosarcomas.

Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

Adaptive history of single copy genes highly expressed in the term human placenta.

Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

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

Recurring mutations found by sequencing an acute myeloid leukemia genome.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

Molecular tumor profiling: translating genomic insights into clinical advances.

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

A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.