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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A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.
PMID 19860899 · PMC2774331 · BMC genomics · 2009 · 8 claims · 6 setups
HaloCHIP is a functional antibody-free alternative to ChIP that uses covalent capture of HaloTag-fusion protein-DNA complexes on HaloLink resin
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Quantitative phosphoproteomics by mass spectrometry: past, present, and future.
PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups
Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS
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Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.
PMID 19929607 · PMC2931417 · Expert review of proteomics · 2009 · 8 claims · 8 setups
Serine/threonine phosphorylation widely functions to modulate protein-protein interactions (PPIs) across signaling systems
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Has reproduction · 96
Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.
PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups
ID-seq combines DNA-tagged antibodies with high-throughput sequencing to enable large-scale, high-dimensional, multiplexed (phospho-)protein phenotyping in fixed cell populations across many samples in parallel.
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An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.
PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups
The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups
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A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.
PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups
FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver
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Locus-specific and activity-independent gene repositioning during early tumorigenesis.
PMID 18195100 · PMC2213600 · The Journal of cell biology · 2008 · 7 claims · 6 setups
The genome undergoes global spatial reorganization during both normal and tumorigenic mammary epithelial differentiation, as shown by reduced nucleolar number.
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Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.
PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups
DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases
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Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.
PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups
Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.
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Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.
PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups
Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.
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A new era for proteomics research?
PMID 19014405 · PMC2614486 · Genome biology · 2008 · 8 claims · 8 setups
Refined mass spectrometry instrumentation and software now make whole-proteome coverage of model organisms in a single experiment conceivable
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Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.
PMID 19834888 · PMC4302342 · Proteomics · 2009 · 7 claims · 7 setups
BioCAT (biotin tagging + AACT) enables highly sensitive and accurate single-step screening of mammalian protein-protein interactions without establishing a stable cell line
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CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.
PMID 16892042 · PMC2360640 · British journal of cancer · 2006 · 6 claims · 6 setups
CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines
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New perspectives on an old disease: proteomics in cancer research.
PMID 17472735 · PMC1895992 · Genome biology · 2007 · 8 claims · 8 setups
The HUPO Plasma Proteome Project has catalogued over 3,020 non-redundant gene products (>7,000 proteins/isoforms) in human plasma, many originating from tissues/organs rather than being plasma-intrinsic.
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Has reproduction · 68
Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.
PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups
LTR8B is a placentally-relevant cis-regulatory element (CRE), notably within the PSG array
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Has reproduction · 92
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia.
PMID 32581241 · PMC7314847 · Nature communications · 2020 · 8 claims · 8 setups
IL7R interacts/colocalizes with CXCR4 on the cell surface, recruiting BCR-ABL1 and JAK kinases into close proximity to form a platform for transformation
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Has reproduction · 90
The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.
PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups
Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.
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Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.
PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups
The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence
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HUPO Highlights.
PMID 19862759 · PMC4594800 · Proteomics · 2009 · 8 claims · 8 setups
Mass spectrometry analysis of human liver reference samples (French Reference liver + Huh7 hepatoma cells) achieves substantial human genome coverage via PeptideAtlas processing
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Has reproduction · 69
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.
PMID 23222129 · PMC3553938 · Nucleic acids research · 2013 · 8 claims · 7 setups
NusA interacts with RNAP ubiquitously throughout the M. tuberculosis chromosome and its ChIP-seq profile mirrors RNAP distribution in both exponential and stationary phase, despite NusA not binding DNA directly.