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 173

Assay: gfp+ ✕ Clear

Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

PMID 18362173 · PMC2292215 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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Somatic JAK1 mutations occur in ALL and are more prevalent among adult T-cell precursor ALL (T-ALL) than B-ALL

genomic jak1-deficient u4c bw5147 dhplc stat1 cytokine-independent
P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

PMID 20046837 · PMC2798614 · PloS one · 2009 · 8 claims · 8 setups

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p19 regulates telomerase activity through its interaction with p73α/β proteins

yeast hela yeast facs pkc
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation
Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

PMID 42246540 · PMC13249099 · Investigative ophthalmology & visual science · 2026 · 8 claims · 7 setups

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ATF4 and BACH1 are identified as bZIP protein interactors of NRL

y2hgold hek293 p28 flow-sorted yeast co-immunoprecipitation immunofluorescence
De novo H3.3K27M-altered diffuse midline glioma in human brainstem organoids to dissect GD2 CAR T cell function.

PMID 41492091 · PMC12948678 · Nature cancer · 2026 · 8 claims · 8 setups

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FGF4 supplementation during organoid patterning specifically induces pontine/rostral hindbrain brainstem identity

hes brainstem day developing bulk immunofluorescence scrna-seq
Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

PMID 41529688 · PMC7618834 · Cell genomics · 2026 · 8 claims · 7 setups

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Sex differences in the Drosophila central brain do not result from large-scale transcriptional reprogramming, but from selective modifications within shared developmental lineages mediated by dsx and fru.

drosophila central dsx+ dsx-gal4>mcd8 single-cell differential scenic
Rtf1-dependent transcriptional pausing regulates cardiogenesis.

PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

zebrafish embryo embryonic mescs crispr situ shrna
CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance.

PMID 41564866 · PMC12866162 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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CHD1 and MAP3K7 loss additively sensitizes cancer cells to IFN-γ-induced death

a375 crc-9 ht-29 vcap whole-genome autologous incucyte
Intestinal macrophages modulate synucleinopathy along the gut-brain axis.

PMID 41606336 · PMC12960212 · Nature · 2026 · 8 claims · 8 setups

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ME-Macs engulf misfolded, aggregated αS and modulate αS pathology and neurodegeneration in PD mouse models

3kl sorted me-macs snca immunohistochemistry digital mass
Notch3 regulates pericyte phenotypic plasticity in colorectal cancer.

PMID 41618002 · PMC12960917 · Communications biology · 2026 · 8 claims · 8 setups

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Murine tumor pericytes originate from normal tissue-resident pericytes that proliferate inside tumors

aom crc pdgfrβ-creert2 notch3-creert2 scrna-seq facs lineage
CITED2 is a druggable epigenetic switch coupling neuronal maturation to regenerative decline.

PMID 41731079 · PMC13083982 · EMBO molecular medicine · 2026 · 8 claims · 8 setups

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The transition from immature non-polarized to mature polarized DRG neurons (E12.5-E17.5) is associated with loss of gene expression signatures needed for regenerative growth competence.

drg sciatic rna-seq integrated immunofluorescence
Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution.

PMID 41738738 · PMC12935429 · eLife · 2026 · 8 claims · 8 setups

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LS-MPRA (BAC-based) and d-MPRA (systematic mutagenesis) are complementary methods for unbiased, high-resolution mapping of cis-regulatory modules.

mus e14 retina candidate ls-mpra single-cell individual
Splicing variants in MYRF cause partial loss of function in the retinal pigment epithelium leading to nanophthalmos.

PMID 41746734 · PMC13043084 · JCI insight · 2026 · 8 claims · 8 setups

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The dG-MYRF C-terminal frameshift variant undergoes normal homotrimerization, cleavage, and nuclear localization but shows reduced steady-state levels of the C-terminal cleavage product and decreased transcriptional activation of target genes.

arpe-19 myrf rpe e17.5 immunofluorescence computational cycloheximide
Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites.

PMID 41778583 · PMC12959880 · eLife · 2026 · 8 claims · 8 setups

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H3K115ac is enriched at the TSS of active CpG island (CGI) promoters, far more than non-CGI promoters

embryonic mescs synthetic mesc chip-seq atac-seq dot
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
The many uses of a genome sequence.

PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

recombinant mammalian chromosome chimpanzee x-ray quantitative tiling
Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

PMID 33837217 · PMC8035321 · Nature communications · 2021 · 8 claims · 8 setups

Has reproduction · 68

MOCCI (encoded by C15ORF48) is a mito-SEP upregulated during inflammation and infection that promotes host-protective resolution

aortic failing colon hek293t ribo-seq wgcna-gsea gene
Core transcriptional signatures of phase change in the migratory locust.

PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups

Has reproduction · 60

PhaseCore genes, identified via AC-PCA across developmental, tissue, and time-course datasets, predict locust phase status (gregarious vs. solitary) with over 87.5% accuracy

locusta bulk interference transcriptional
Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.

PMID 37217248 · PMC10231005 · Journal for immunotherapy of cancer · 2023 · 8 claims · 8 setups

Has reproduction · 76

High expression of IFN-I signaling/response genes (IFNAR1, IFNAR2, STAT1, MX1, OAS1) predicts favorable relapse-free survival in B-ALL patients

cog b-all eμ-myc crispra gene-expression-based flow mass

Experiments

Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

Neuroscience in the era of functional genomics and systems biology.

Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

De novo H3.3K27M-altered diffuse midline glioma in human brainstem organoids to dissect GD2 CAR T cell function.

Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

Rtf1-dependent transcriptional pausing regulates cardiogenesis.

CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance.

Intestinal macrophages modulate synucleinopathy along the gut-brain axis.

Notch3 regulates pericyte phenotypic plasticity in colorectal cancer.

CITED2 is a druggable epigenetic switch coupling neuronal maturation to regenerative decline.

Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution.

Splicing variants in MYRF cause partial loss of function in the retinal pigment epithelium leading to nanophthalmos.

Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites.

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

The many uses of a genome sequence.

Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

Core transcriptional signatures of phase change in the migratory locust.

Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.