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 · 78
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups
A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors
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Has reproduction · 100
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups
TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.
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Full-text index only
GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.
PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups
GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Has reproduction · 58
Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.
PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups
Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.
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Has reproduction · 68
Bayesian transcriptome assembly.
PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups
Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.
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Has reproduction · 62
Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).
PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups
TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR
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Has reproduction · 76
PI3K inhibitors protect against glucocorticoid-induced skin atrophy.
PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 7 claims · 8 setups
PI3K/mTOR/Akt inhibitors are a pharmacological class that represses glucocorticoid-induced REDD1 and FKBP51 expression, identified via LINCS drug-repurposing screen.
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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
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Has reproduction · 97
Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.
PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups
The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)
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Has reproduction · 51
Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.
PMID 32542016 · PMC7295234 · PloS one · 2020 · 6 claims · 8 setups
Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC versus normal liver at mRNA and protein levels
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Has reproduction · 88
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.
PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups
COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.
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Has reproduction · 43
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.
PMID 34089405 · PMC8179884 · Rice (New York, N.Y.) · 2021 · 8 claims · 7 setups
N22 performs better under dual (low N + low water) stress owing to better root architecture, chlorophyll/porphyrin synthesis and oxidative stress management
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Has reproduction · 78
Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia.
PMID 34709177 · PMC8553341 · eLife · 2021 · 8 claims · 5 setups
A 120-gene endometrial transcriptomic fingerprint encodes defective decidualization associated with severe preeclampsia.
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Has reproduction · 83
Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.
PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 7 claims · 4 setups
A metabolite-centric reporter pathway analysis (RPAm) can infer cold-stress-associated metabolites and pathways in Arabidopsis directly from transcriptome data without metabolome data
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Has reproduction · 100
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.
PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups
A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction · 50
Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.
PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups
lncRNA-mRNA ceRNA networks differ substantially between control and cytokine-treated islet exosomes, sharing lncRNAs more than mRNAs, implying state-dependent regulatory functions
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Has reproduction · 100
Comprehensive data for studying serum exosome microRNA transcriptome in Parkinson's disease patients.
PMID 39406833 · PMC11480472 · Scientific data · 2024 · 8 claims · 8 setups
The study presents comprehensive serum exosome miRNA transcriptome data from four independent Japanese cohorts of PD patients and controls.
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Has reproduction · 73
Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.
PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups
Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.