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 · 52
Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.
PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups
A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity
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Has reproduction · 75
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.
PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups
Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.
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Has reproduction · 58
A comparative study of techniques for differential expression analysis on RNA-Seq data.
PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups
edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.
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Has reproduction · 37
RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).
PMID 36429012 · PMC9688714 · Cells · 2022 · 6 claims · 7 setups
RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression.
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Has reproduction · 75
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups
AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles
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Has reproduction · 93
Under the Shadow: Old-biased Genes Are Subject to Weak Purifying Selection at Both the Tissue- and Cell Type-Specific Levels.
PMID 41092135 · PMC12569596 · Genome biology and evolution · 2025 · 8 claims · 6 setups
Age-related decrease in transcriptome conservation (ADICT) is commonly found in ageing tissues of nonmammalian species (chicken brain, killifish liver and skin, fruit fly brain).
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Has reproduction · 68
Microglia maintain structural integrity during fetal brain morphogenesis.
PMID 38309258 · PMC10869139 · Cell · 2024 · 8 claims · 8 setups
ATM-like microglia accumulate at two embryonic cortical boundaries, the cortico-striato-amygdalar boundary (CSA) and cortico-septal boundary (CSB)
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Has reproduction · 50
Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.
PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 6 claims · 7 setups
A computational method using high-quality scRNA-seq reference data can estimate per-sample, per-cell-type off-target contamination coefficients in sctRNA-seq datasets.
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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 · 84
TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.
PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 6 claims · 4 setups
TransOrGAN can infer transcriptomic profiles between any 2 of 9 organs with an average cosine similarity of 0.984 between synthetic and real profiles
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Has reproduction · 63
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.
PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups
More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes
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Has reproduction · 67
Optimal scaling of digital transcriptomes.
PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups
Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.
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Has reproduction · 26
Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.
PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups
The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature
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Has reproduction · 89
miRge 2.0 for comprehensive analysis of microRNA sequencing data.
PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups
miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification
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Has reproduction · 60
Core transcriptional signatures of phase change in the migratory locust.
PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups
PhaseCore genes defined by AC-PCA contribution to phase differentiation predict phase status with >87.5% accuracy
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Has reproduction · 69
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.
PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups
COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity
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Has reproduction · 50
Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.
PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 8 claims · 8 setups
p16+ and p21+ senescent cells are largely distinct, non-overlapping populations across murine and human aging tissues, with only rare double-positive cells
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Has reproduction · 87
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups
mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.
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Has reproduction · 78
Protocol for the generation of single-nuclei RNA-seq libraries and quantification of heterogeneous cell types activated during social interaction.
PMID 39423127 · PMC11532268 · STAR protocols · 2024 · 7 claims · 5 setups
A protocol for dissecting mouse PFC, hippocampus, and cerebellum and generating snRNA-seq libraries can identify neuronal populations activated during social interaction.
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Has reproduction
miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.
PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 6 claims · 5 setups
miRge3.0 with 12 CPUs consistently has the best execution speed compared to miRge2.0, Chimira and sRNAbench