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 · 66
HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.
PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups
HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.
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Has reproduction · 100
Betacoronavirus-specific alternate splicing.
PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups
Genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those in SARS-CoV and MERS, affecting a diverse set of genes and biological functions related to virus biology.
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Has reproduction · 90
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.
PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)
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Has reproduction · 66
Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.
PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups
At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls
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Gene expression and isoform variation analysis using Affymetrix Exon Arrays.
PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups
The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.
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Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.
PMID 18922159 · PMC2614521 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups
PGRMC1 protein spots are differentially abundant between ER-negative and ER-positive breast tumors, with two of three spots more abundant in ER-negative tumors
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Has reproduction · 83
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.
PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups
The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.
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Has reproduction · 59
Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.
PMID 39057099 · PMC11276454 · Current issues in molecular biology · 2024 · 8 claims · 8 setups
PTBP1 is significantly upregulated across multiple cancer types including LUAD, and higher PTBP1 levels are associated with worse LUAD patient survival
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Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.
PMID 19943934 · PMC2794290 · BMC cancer · 2009 · 8 claims · 5 setups
Hundreds of genes differentiate GISTs according to KIT versus PDGFRA mutation and expression status, despite no discriminative profile for clinical/pathological parameters.
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Has reproduction · 71
Perturbation of placental protein glycosylation by endoplasmic reticulum stress promotes maladaptation of maternal hepatic glucose metabolism.
PMID 36660474 · PMC9843443 · iScience · 2023 · 8 claims · 8 setups
ER stress reduces the complexity and sialylation of trophoblast protein N-glycosylation
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Has reproduction · 30
SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.
PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 7 claims · 5 setups
Short-term heat stress strongly and specifically activates Hsps, Hsfs, FKBPs, calcium signaling, glutathione S-transferase, photosynthesis, and phytohormone signaling genes.
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Has reproduction · 83
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups
Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.
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The UCSC Genome Browser Database: update 2006.
PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups
The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.