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 · 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 · 96
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.
PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups
An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.
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Has reproduction · 83
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.
PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups
scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach
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Has reproduction · 91
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.
PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups
DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.
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Has reproduction · 80
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.
PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 7 claims · 8 setups
C3 PLP2+ Tumor Epithelial Progenitor Cells are a key subpopulation that drives differentiation and progression of cervical carcinoma
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups
A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).
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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 · 73
Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.
PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups
Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.
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Has reproduction · 88
From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 8 claims · 7 setups
Flower buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are each defined by expression of genes in specific pathways, and the transcriptional state accurately captures the dormancy state.
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 78
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups
CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.
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Has reproduction · 71
Comprehensive comparison of gene expression diversity among a variety of human stem cells.
PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 6 claims · 7 setups
iPSC gene expression is more strongly influenced by tissue origin than other stem cell types, whereas ESCs and somatic stem cells (MSCs, HSCs) are more strongly impacted by culture condition.
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Has reproduction · 47
Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq.
PMID 33441952 · PMC7806779 · Scientific reports · 2021 · 8 claims · 5 setups
CDK12, ERBB2, and CLDN11 are overexpressed in metastatic lymph node gastric cancer and serve as candidate lymph node metastasis marker genes.
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Has reproduction · 93
Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.
PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups
Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species
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Has reproduction · 63
Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution.
PMID 35977485 · PMC9644345 · Cell reports · 2022 · 8 claims · 8 setups
Bmp4 treatment instructs ESCs to downregulate pluripotency genes and upregulate genes associated with formative pluripotency and fate specification
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Has reproduction · 85
Prediction of condition-specific regulatory genes using machine learning.
PMID 32329779 · PMC7293043 · Nucleic acids research · 2020 · 8 claims · 6 setups
ConSReg integrates expression, DAP-seq TF-DNA binding, and ATAC-seq open chromatin data into machine learning models to predict condition-specific regulatory genes
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Has reproduction · 48
Rbfox2 controls autoregulation in RNA-binding protein networks.
PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups
Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.
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Has reproduction · 67
Reducing language barriers, promoting information absorption, and communication using fanyi.
PMID 39039634 · PMC11332769 · Chinese medical journal · 2024 · 7 claims · 3 setups
The fanyi R package retrieves gene information from NCBI and translates it into multiple languages using AI-driven online translation services
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Has reproduction · 80
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.
PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups
PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.