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).
-
Has reproduction · 91
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.
PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups
De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads
-
Has reproduction · 94
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.
PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 5 setups
EiaD is a reproducible, versioned RNA-seq transcriptome dataset combining 916 healthy human eye samples and 1375 GTEx body samples across 19 eye and 54 body tissues, built with a Snakemake pipeline and served as a single SQLite database.
-
Full-text index only
Heritable Genetic Effects Caused by a Single Generation of Captive Breeding.
PMID 42015961 · PMC13093589 · Evolutionary applications · 2026 · 8 claims · 6 setups
Hundreds of genes (385) are differentially expressed between offspring of first-generation hatchery (H×H) and natural-origin (N×N) steelhead reared in a common environment
-
Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
-
Full-text index only
Identification of Radiation-Induced Injury Pathways and Hub Genes from RNA-Seq Data Based on Integrative Bioinformatics Approach.
PMID 42074497 · PMC13116960 · Genes · 2026 · 8 claims · 6 setups
Ionizing radiation induces extensive transcriptome reprogramming in mouse bone marrow HSCs 3 days after whole-body irradiation.
-
Has reproduction · 90
PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.
PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups
PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.
-
Has reproduction · 50
Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.
PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups
829 genes are overexpressed in regions of increased calcite spicule formation in S. ciliatum, including known sclerocyte-specific biomineralization genes.
-
Full-text index only
Comprehensive stage- and tissue-specific transcriptome of the global ecosystem service insect, marmalade hoverfly Episyrphus balteatus.
PMID 41927565 · PMC13216633 · Scientific data · 2026 · 8 claims · 8 setups
Generated a comprehensive developmental- and tissue-resolved transcriptome dataset for Episyrphus balteatus as a community resource
-
Has reproduction · 90
Inferring a spatial code of cell-cell interactions across a whole animal body.
PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups
cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells
-
Has reproduction · 69
A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups
Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.
-
Full-text index only
Temporal multiomics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation.
PMID 41545424 · PMC12920657 · Scientific data · 2026 · 8 claims · 8 setups
Generated a high-resolution, time-resolved multi-omics dataset (RNA-seq, ribosome profiling, and quantitative proteomics) tracking mRNA, translation, and protein dynamics across hESC differentiation into definitive endoderm and polyhormonal pancreatic cells
-
Full-text index only
Transcriptomic insights into thermal manipulation and heat stress in skeletal muscles of broiler chickens.
PMID 41905070 · PMC13054079 · Poultry science · 2026 · 6 claims · 5 setups
Acute HS induces pronounced transcriptional changes including activation of immune signaling and stress-responsive pathways and suppression of metabolic/energy-related processes
-
Has reproduction · 89
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.
PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 7 setups
There is a general lack of global gene regulation across re-analyzed Wolbachia transcriptomes, with the exception of a weak transcriptional response upregulating ribosomal proteins in early larval stages.
-
Has reproduction · 63
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.
PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups
>700 tissue-specific transcriptomes generated from w1118 and 141 DGRP Drosophila lines, forming a circadian gene expression atlas
-
Has reproduction · 71
Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome.
PMID 36611783 · PMC9817706 · Animals : an open access journal from MDPI · 2023 · 8 claims · 6 setups
1442 genes were differentially expressed in AS broiler lung vs normal lung (614 up-regulated, 828 down-regulated)
-
Has reproduction · 82
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.
PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups
An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.
-
Full-text index only
Blood feeding triggers the terminal differentiation of precursor cells in tick salivary glands.
PMID 41880507 · PMC13015885 · Science advances · 2026 · 8 claims · 8 setups
Unfed I. scapularis salivary glands contain a conserved population of undifferentiated precursor cells.
-
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, identified via AC-PCA across developmental, tissue, and time-course datasets, predict locust phase status (gregarious vs. solitary) with over 87.5% accuracy
-
Has reproduction · 69
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.
PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups
Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis
-
Has reproduction · 88
The Drosophila estrogen-related receptor promotes triglyceride storage within the larval fat body.
PMID 40288680 · PMC12155637 · Journal of lipid research · 2025 · 8 claims · 8 setups
dERR autonomously promotes TAG accumulation within larval fat body cells