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 27

System / cell line: normalized ✕ Assay: induced ✕ Clear

Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

PMID 17485517 · PMC2118573 · The Journal of experimental medicine · 2007 · 8 claims · 8 setups

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AID mRNA is aberrantly expressed in Ph+ ALL but largely absent in Ph- ALL

normal ph+ semiquantitative western rt-pcr
Anesthetics impact the resolution of inflammation.

PMID 18382663 · PMC2268966 · PloS one · 2008 · 8 claims · 8 setups

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Lidocaine delays and blocks key events in the resolution of acute inflammation

peritoneal cell-free zymosan-induced lipid apoptosis
Magnetization transfer imaging in 'premanifest' Huntington's disease.

PMID 19823894 · PMC2837878 · Journal of neurology · 2010 · 8 claims · 4 setups

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MTI parameters (mean MTR and normalized peak height) of whole brain, grey matter and white matter did not differ significantly between premanifest HD carriers and non-carriers

premanifest magnetization 3d-t1-weighted clinical
Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

blood platelets platelet-rich platelet whole-genome quantitative flow
The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

PMID 12036445 · PMC5927037 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 5 setups

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SNI (elevated spontaneous point mutation rate without microsatellite instability) is present in rat mammary carcinoma cell lines and human breast cancer cell lines

mammary same normal pcr-sscp direct quantitative
Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer.

PMID 18690643 · PMC3970323 · Proteomics · 2008 · 8 claims · 5 setups

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N-linked glycan biosynthetic enzyme transcript profiles in normal mouse and human ovarian tissue are similar, indicating species conservation

ovarian qrt-pcr lectin con
Single-cell transcriptomics reveals keratinocyte dynamic processes associated with S100a4 expression in psoriasiform dermatitis.

PMID 41660613 · PMC12876221 · Frontiers in immunology · 2025 · 7 claims · 8 setups

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S100a4 knockout mice show significant pathological improvement in psoriasis-like lesions, including reduced inflammatory cell infiltration and decreased epidermal hyperplasia

c57bl skin dorsal dcmo crispr western imiquimod-induced
miR-203 facilitates timely cell fate transitions via epigenetic modulation during early embryogenesis.

PMID 41811946 · PMC12978216 · Science advances · 2026 · 8 claims · 8 setups

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miR-203 is required for a timely totipotency-to-pluripotency transition during early mouse embryogenesis

preimplantation 8-cell mice mir-203 qrt-pcr genotyping time-lapse
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

Has reproduction · 68

LTR8B is a placentally-relevant cis-regulatory element (CRE), notably within the PSG array

sghpl-4 bewo recombinant serum chip-exonuclease transient quantitative
RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

PMID 36429012 · PMC9688714 · Cells · 2022 · 7 claims · 7 setups

Has reproduction · 37

RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression

brain rna-edited brain-isolated naïve rna-seq pathway pcr
Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.

PMID 36591261 · PMC9797520 · Frontiers in immunology · 2022 · 8 claims · 6 setups

Has reproduction · 50

CCR2hi and CCR2lo periarticular bone marrow OCP subsets show a disparate transcriptome (863 differentially expressed genes)

sorted rna-seq periarticular bulk gene flow
Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 8 claims · 8 setups

Has reproduction · 68

The integrated stress response (ISR) induces CRC cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

ht29-derived ht29 nod rna-seq faire-qpcr chip-seq
Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

Has reproduction · 58

SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

rms rh4 h3k27ac pooled chip-seq
A large-scale proteomic analysis of human embryonic stem cells.

PMID 18162134 · PMC2211323 · BMC genomics · 2007 · 8 claims · 5 setups

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Two large-scale western blot systems (PowerBlot, Kinexus) identify over 600 proteins expressed in undifferentiated hESCs across 18 functional classes

bg01 bg03 hescs powerblot kinexus immunofluorescence
The genomic analysis of lactic acidosis and acidosis response in human cancers.

PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

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Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

mammary hmec gene breast gene real-time bayesian
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr
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
TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

Has reproduction · 80

TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

imr90 hct116 chip-seq rna-seq atac-seq
Genome-scale modeling identifies dynamic metabolic vulnerabilities during the epithelial to mesenchymal transition.

PMID 39730911 · PMC11681178 · Communications biology · 2024 · 8 claims · 8 setups

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EMT involves temporal, stage-specific metabolic reprogramming with distinct dependencies in glycolysis and glutamine metabolism.

a549 recon1 cancer lung bulk single-cell genome-scale
Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

PMID 41939867 · PMC13043422 · Frontiers in immunology · 2026 · 7 claims · 8 setups

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CXCL13, IL33, TLR4, and IGF1 are core IPF genes consistently linked to immune infiltration and fibrotic remodeling across bulk, single-cell, spatial, and blood multi-omics data

lung candidate bulk normalized bulk ppi machine

Experiments

Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

Anesthetics impact the resolution of inflammation.

Magnetization transfer imaging in 'premanifest' Huntington's disease.

Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer.

Single-cell transcriptomics reveals keratinocyte dynamic processes associated with S100a4 expression in psoriasiform dermatitis.

miR-203 facilitates timely cell fate transitions via epigenetic modulation during early embryogenesis.

Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.

Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

A large-scale proteomic analysis of human embryonic stem cells.

The genomic analysis of lactic acidosis and acidosis response in human cancers.

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

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

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

Genome-scale modeling identifies dynamic metabolic vulnerabilities during the epithelial to mesenchymal transition.

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.