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 19

System / cell line: t-cells ✕ Assay: mapping ✕ Clear

Global mapping of the topography and magnitude of proteolytic events in apoptosis.

PMID 18724940 · PMC2597167 · Cell · 2008 · 7 claims · 6 setups

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PROTOMAP, a method combining 1D SDS-PAGE fractionation with LC-MS/MS-derived sequence coverage and spectral counting visualized as 'peptographs', enables global mapping of proteolytic topography and magnitude

jurkat sds-page fragmentation caspase-3
Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 7 setups

Has reproduction · 77

HIV-1 recurrently integrates into genes that are proximal to super-enhancer (SE) genomic elements in both patients and in vitro T cell cultures.

activated cd4+ cd3 uninfected hiv-1 chip-seq rna-seq
Nucleosome deposition and DNA methylation at coding region boundaries.

PMID 19723310 · PMC2768978 · Genome biology · 2009 · 8 claims · 8 setups

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Nucleosomes and DNA methylation form distinct peaks just downstream of the start codon and just upstream of the stop codon, marking both ends of protein coding units genome-wide.

yeast drosophila resting naive nucleosome methylation pol
X-linked hyper IgM (HIGM1) in an African kindred: the first report from South Africa.

PMID 14641931 · PMC317313 · BMC pediatrics · 2003 · 7 claims · 5 setups

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This is the first fully characterized South African family with X-linked hyper-IgM syndrome (HIGM1)

activated pbmcs genomic pcr flow rt-pcr long-range
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

subset drosophila ensembl lc-ms icat peptide-to-genome
G-quadruplexes in promoters throughout the human genome.

PMID 17169996 · PMC1802602 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Promoter regions (1 kb upstream of TSS) are significantly enriched in quadruplex motifs (PQS) relative to the rest of the genome

genome quiescent gene synthetic computational nuclease gene
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

embryonic neural t-cells mm8 chip-seq chip-chip pwm
Systems biology: where it's at in 2005.

PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

saccharomyces drosophila environmental literature systematic genome-wide
The PeptideAtlas project.

PMID 16381952 · PMC1347403 · Nucleic acids research · 2006 · 8 claims · 5 setups

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PeptideAtlas provides an automated repository that identifies peptides by MS/MS, statistically validates identifications, and maps them to eukaryotic genomes to enable data exchange and integration with genomic data.

plasma drosophila yeast tandem sequence
Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

Has reproduction · 88

CD39+CD8+ TILs are a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells within ccRCC tumors

ccrcc tumor-reactive cd39 caix-specific single-cell bulk co-culture
JunB Is Critical for Survival of T Helper Cells.

PMID 35837408 · PMC9273772 · Frontiers in immunology · 2022 · 7 claims · 7 setups

Has reproduction · 69

JunB is required for clonal expansion of Th1, Th2, and Th17 cells

ot-ii junb naive th1 flow adoptive th1
Interactome networks: the state of the science.

PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

genes tnfα orf proteins yeast tandem interference
Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

PMID 19757078 · PMC2843092 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2009 · 7 claims · 8 setups

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Human B cells express one CB2 transcript while mouse B cells express three CB2 transcripts

splenocytes pbmc-derived splenic genbank race pcr quantitative
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

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Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq
Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 51

Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl
Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

PMID 18560825 · PMC2493868 · Immunogenetics · 2008 · 8 claims · 8 setups

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Neither transcriptional profiling alone nor genetic linkage analysis alone has been an effective approach to identify genes or gene networks that specify stemness or initiate differentiation/lineage specification.

escs fibroblasts hematopoietic bxd transcriptional forced long-term
In silico promoters: modelling of cis-regulatory context facilitates target predictio.

PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

serca2 rantes genes podocyte-associated literature-based promoter cross-referenced
Tipping the balance in autoimmune disease.

PMID 18001485 · PMC2246277 · Genome biology · 2007 · 8 claims · 8 setups

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Human autoimmune diseases are fundamentally diseases of immune dysfunction, evidenced by predisposing genes being immune-function genes, some shared and some unique across MS, T1D, SLE, CD and RA

patients congenic nzm2410 mrl-lpr snp induced genetic
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

Has reproduction · 85

Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

normal er+ epithelial malignant single-cell spatial copy

Experiments

Global mapping of the topography and magnitude of proteolytic events in apoptosis.

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

Nucleosome deposition and DNA methylation at coding region boundaries.

X-linked hyper IgM (HIGM1) in an African kindred: the first report from South Africa.

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

G-quadruplexes in promoters throughout the human genome.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

Systems biology: where it's at in 2005.

The PeptideAtlas project.

Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

JunB Is Critical for Survival of T Helper Cells.

Interactome networks: the state of the science.

Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

In silico promoters: modelling of cis-regulatory context facilitates target predictio.

Tipping the balance in autoimmune disease.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.