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 4

System / cell line: t47d ✕ Assay: gene ✕ Clear

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

Full-text index only

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
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 7 claims · 8 setups

Has reproduction · 77

PredTAD, a Gradient Boosting Machine model using epigenomic and genomic features plus neighboring-bin information, classifies 10 kb genomic regions as TAD boundary or non-boundary across normal and breast cancer cell lines.

mcf10a t47d gm12878 mcf7 hi-c chip-seq atac-seq
Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

PMID 28446242 · PMC5406893 · Genome medicine · 2017 · 7 claims · 6 setups

Has reproduction · 92

Breast tumors exhibit two discrete GFRN activity phenotypes: a 'survival phenotype' with concordant HER2/IGF1R/AKT activation and a 'growth phenotype' with concordant EGFR/KRAS(G12V)/RAF1/BAD activation, which are typically mutually exclusive.

mammary tcga hmecs breast rna-sequencing pathway western
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

Full-text index only

Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp

Experiments

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

PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.