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).
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Has reproduction · 79
The relationship between PLOD1 expression level and glioma prognosis investigated using public databases.
PMID 34040895 · PMC8127981 · PeerJ · 2021 · 8 claims · 8 setups
PLOD1 mRNA expression is significantly higher in glioma tissue than in normal brain tissue
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Has reproduction · 45
RNA structure maps across mammalian cellular compartments.
PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups
icSHAPE can map RNA secondary structure in vivo across three subcellular compartments (chromatin, nucleoplasm, cytoplasm) in both human and mouse cells
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Has reproduction · 67
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
Trem2 R47H knock-in mice show gene dose-dependent decreased Trem2 expression in hippocampus, largely due to altered splicing
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Has reproduction · 100
Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.
PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups
The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types
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Has reproduction · 94
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.
PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups
HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)
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Has reproduction
The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.
PMID 41131451 · PMC12551222 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 8 setups
Significant genetic introgression from Chinese pigs into commercial European pig lines is confirmed using SNP chip and resequencing data.
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Has reproduction · 95
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.
PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups
RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA
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Has reproduction · 70
Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility.
PMID 34021225 · PMC8140134 · Scientific reports · 2021 · 8 claims · 8 setups
Sulfate-reducing Desulfovibrio are the key players responsible for H2S production in swine manure slurry
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Has reproduction · 50
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.
PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 7 claims · 6 setups
MEDUSA correctly identifies more species than MEGAN 6 CE, especially less abundant species.
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Has reproduction · 61
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.
PMID 35584008 · PMC9465075 · Microbial genomics · 2022 · 8 claims · 7 setups
RegulonDB 11.0 is a radical upgrade offering access to more than 2000 high-throughput datasets on transcriptional regulation in E. coli K-12.
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Has reproduction · 100
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.
PMID 36123620 · PMC9487059 · BMC bioinformatics · 2022 · 6 claims · 8 setups
msPIPE is a new end-to-end pipeline integrating pre-processing, alignment & methylation calling, and downstream DNA methylation analysis (profiling, HMR, DMR, functional enrichment) with publication-quality figure output for WGBS data
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Has reproduction · 55
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.
PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups
Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo
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Has reproduction · 86
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.
PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups
CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome
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Has reproduction · 76
Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.
PMID 35806266 · PMC9267015 · International journal of molecular sciences · 2022 · 8 claims · 7 setups
mCCD cl1 cells mount a broad transcriptional response to 24 h hypoxia (0.2% O2), with 3086 genes differentially expressed
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Association of p53 gene mutations with short survival in pancreatic adenocarcinoma.
PMID 7730141 · PMC5920762 · Japanese journal of cancer research : Gann · 1995 · 8 claims · 4 setups
p53 gene mutations were detected in 16 of 37 (43%) pancreatic adenocarcinomas by SSCP and direct sequencing
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The promoter and the enhancer region of the KLK 3 (prostate specific antigen) gene is frequently mutated in breast tumours and in breast carcinoma cell lines.
PMID 10188912 · PMC2362704 · British journal of cancer · 1999 · 7 claims · 5 setups
No mutations were found in the protein-coding exons of the PSA gene in breast tumours or cell lines
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Comparative genomics and understanding of microbial biology.
PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups
GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.
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Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.
PMID 11532213 · PMC55326 · Genome biology · 2001 · 7 claims · 5 setups
The human genome contains fewer than 50 functional nuclear receptors, far fewer than C. elegans and about twice as many as Drosophila
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SARS--beginning to understand a new virus.
PMID 15035025 · PMC7097337 · Nature reviews. Microbiology · 2003 · 8 claims · 8 setups
A previously unknown coronavirus (SARS-CoV) was isolated from FRhK-4 and Vero E6 cells inoculated with clinical specimens from SARS patients and identified as the causative agent of SARS
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Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.
PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups
An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.