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 · 62
The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.
PMID 38537644 · PMC11063626 · Cell reports · 2024 · 8 claims · 8 setups
The natural (non-sterilized) Clue Field soil microbiome reduces Striga attachment to sorghum roots compared to gamma-sterilized soil
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Has reproduction · 69
Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.
PMID 39009986 · PMC11247842 · Genetics, selection, evolution : GSE · 2024 · 5 claims · 8 setups
Meta-analysis of GWAS across six dairy cattle breeds identifies 58 lead markers associated with clinical mastitis and somatic cell score
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Has reproduction · 66
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.
PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups
A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons
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Has reproduction · 70
Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.
PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups
AR chromatin binding is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites (ARBS) shared by half of the 88 tumors analyzed
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Has reproduction · 50
Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.
PMID 36450262 · PMC9792173 · Cell reports · 2022 · 8 claims · 6 setups
IL-21-producing Tfh CD4 T cells repopulate after CD4 depletion but remain at reduced frequency compared with control mice
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Has reproduction · 76
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.
PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups
DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples
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Has reproduction · 45
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
PMID 29451882 · PMC5815590 · PloS one · 2018 · 8 claims · 7 setups
This is the first de novo transcriptomic analysis of C. officinalis leaf and fruit tissue, performed using the Illumina HiSeq 4000 platform.
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Has reproduction
Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.
PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 8 claims · 8 setups
114 CNGC genes were identified across the genomes of four cotton species (G. arboreum, G. raimondii, G. barbadense, G. hirsutum)
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Has reproduction · 59
Comparing time series transcriptome data between plants using a network module finding algorithm.
PMID 31164912 · PMC6544932 · Plant methods · 2019 · 8 claims · 6 setups
Converting gene expression patterns into co-expression networks and applying a cross-species network module finding algorithm (OrthoClust with simulated annealing) solves the problem of matching developmental stages between two species without requiring one-to-one stage mapping.
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Has reproduction · 10
Effect of PAIP1 on the metastatic potential and prognostic significance in oral squamous cell carcinoma.
PMID 35153296 · PMC8841500 · International journal of oral science · 2022 · 8 claims · 8 setups
PAIP1 mRNA and protein levels are increased in OSCC/HNSCC tissues and cell lines compared to normal tissue/cells
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Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups
A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.
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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 · 7 claims · 7 setups
sctRNA-seq datasets (particularly LCM-seq) show measurable off-target mRNA contamination from surrounding cell types
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Has reproduction · 89
Depletion of HIV reservoir by activation of ISR signaling in resting CD4(+)T cells.
PMID 36590168 · PMC9800255 · iScience · 2023 · 8 claims · 8 setups
Activation of ISR/ATF4 signaling (via HA15) reverses HIV latency in Jurkat models of HIV latency (J-Lat A1, 2D10)
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Has reproduction · 100
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.
PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups
44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.
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Has reproduction · 79
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups
196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions
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Has reproduction · 76
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.
PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups
Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock
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Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning B. taurus samples to UOA_Brahman_1 detects up to 5 million more SNVs than aligning to ARS_UCD1.2, and aligning B. indicus samples to ARS_UCD1.2 detects 1.5 million more SNVs than aligning to UOA_Brahman_1, demonstrating reference-genome bias.
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Has reproduction · 91
GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau.
PMID 40204713 · PMC11982250 · Nature communications · 2025 · 8 claims · 7 setups
GRAMD1B is increased in excitatory neurons of human neural organoids (HNOs) carrying the MAPT R406W mutation
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Has reproduction · 71
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.
PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups
Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics
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Has reproduction · 70
Zebrafish functional xenograft vasculature platform identifies PF-502 as a durable vasculature normalization drug.
PMID 37680473 · PMC10480778 · iScience · 2023 · 8 claims · 8 setups
The zebrafish functional xenograft vasculature platform (zFXVP) enables visualization and quantification of structurally and functionally realistic tumor vasculature formation.