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).

Publications 1.3k Datasets 392.5k Experiments 14

System / cell line: myeloid ✕ Assay: differential ✕ Clear

Genomic expression during human myelopoiesis.

PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

myeloid same cd34+ gene microarray unsupervised sam
A distinct epigenetic signature at targets of a leukemia protein.

PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

32d sequence gene bioinformatic real-time
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

diffuse-type liver renal anaplastic differential proteomic proteomics
Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

Has reproduction · 26

The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

acutely microglia c57bl meta-analysis integration spectral
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups

Has reproduction · 65

comBO is a single iPSC-derived organoid differentiation that generates osteolineage, vascular, lymphoid, and myeloid compartments together

hipsc-derived combo combo-derived healthy-donor flow single-cell confocal
Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

Has reproduction · 70

Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime
Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

nb4 tf1 tracheobronchial moser affymetrix cdna microarray
Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups

Has reproduction · 63

Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.

liver pbmc integrated gene scrna-seq differential ingenuity
Digital sorting of complex tissues for cell type-specific gene expression profiles.

PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

Has reproduction · 85

The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

liver im-9 immune deconvolved microarray simulation roc
Iterative class discovery and feature selection using Minimal Spanning Trees.

PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

simulated breast acute diffuse synthetic cdna microarray
Proteomics technologies and challenges.

PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

serum myeloid formalin-fixed general maldi-tof phage maldi
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

Has reproduction · 76

Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock

tumors metastatic methylation bulk kegg
Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

umbilical ucb zebrafish microarray fluorescence-activated quantitative
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

Has reproduction · 94

Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

nsclc coad brca tcga scrna-seq bulk rna-seq

Experiments

Genomic expression during human myelopoiesis.

A distinct epigenetic signature at targets of a leukemia protein.

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

Digital sorting of complex tissues for cell type-specific gene expression profiles.

Iterative class discovery and feature selection using Minimal Spanning Trees.

Proteomics technologies and challenges.

High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.

Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.