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 517

Assay: expressed ✕ Clear

Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells.

PMID 41485059 · PMC12930946 · Journal of ovarian research · 2026 · 8 claims · 6 setups

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Acute 10 Gy X-ray irradiation does not significantly affect viability (ATP levels, mitochondrial dehydrogenase activity) of cPOCs and mPOCs over 7 days.

kgn cpocs celltiter-glo mtt immunofluorescence
Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

PMID 41612263 · PMC12924552 · BMC biology · 2026 · 8 claims · 6 setups

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Profiling gene expression across 26 life stages of A. millepora and building an interactive Shiny-based tool (DEView) enables comprehensive visualisation of developmental transcriptomic data.

acropora millepora bulk differential pca
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.

PMID 41688823 · PMC12904797 · Nature cell biology · 2026 · 8 claims · 8 setups

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IDR function depends on two distinct but related properties: sequence specificity (motifs) and chemical specificity (distributed multivalent chemistry)

cerevisiae orthologous abf1 fus1-163 plasmid anti-flag proteome-wide
Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.

PMID 41729083 · PMC12956012 · JCI insight · 2026 · 8 claims · 7 setups

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A clonally expanded CD8+GZMK+IFNG+ T cell population (subdivided into IFNGhi and IFNGint groups) is enriched in the EM lesion and shows an inflammatory, tissue-resident phenotype (GZMBlo/PRF1-) resembling tissue-enriched GZMK+ TteK cells

whole-skin cd8+gzmk+ifnghi identified skin scrna-seq pseudobulk immune
Eduomics: a Nextflow pipeline to simulate -omics data for education.

PMID 41816779 · PMC12972896 · NAR genomics and bioinformatics · 2026 · 8 claims · 4 setups

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Eduomics is a Nextflow DSL2 pipeline that automates generation of validated variant-calling and RNA-seq datasets for education while abstracting away technical requirements

chromosome full simulated exome rna-seq pipeline
Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.

PMID 41987828 · PMC13077298 · ISME communications · 2026 · 8 claims · 5 setups

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Transplantation of a microbiome from heat-primed donor clams into non-acclimated recipients is sufficient to enhance host resilience during a subsequent simulated heatwave.

ruditapes philippinarum 16s host enzymatic
STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.

PMID 42044152 · PMC13160441 · PLoS computational biology · 2026 · 8 claims · 8 setups

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STARCall combines image stitching and cross-cycle alignment into a single joint optimization step (via ConStitch) that minimizes both inter-cycle and intra-cycle alignment error.

stem slice a549 u2os image situ simulated
Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

PMID 42064353 · PMC13126010 · Wellcome open research · 2026 · 7 claims · 7 setups

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Deformable gametocytes are immediately infectious upon release from the bone marrow into circulation.

synchronized falciparum blood microsphere bulk exflagellation
ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A.

PMID 42208531 · PMC13261933 · Stem cell reports · 2026 · 8 claims · 8 setups

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ZFHX4 is a super-enhancer-controlled transcription factor induced during mDAN specification

ipsc-derived smnpcs postmortem cut&tag bulk shrna
Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental
Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation.

PMID 41477881 · PMC12850507 · Science (New York, N.Y.) · 2026 · 8 claims · 8 setups

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A haplotype at the 17q22 locus, tagged by the noncoding variant rs17834140-T, is a causal protective variant against CHIP and myeloid malignancies

population hspcs cd34+cd45ra-cd90+ heterozygous gwas atac-seq crispr
TEAD4 and RXRA Regulate the Function of Nucleus Pulposus Cells in Intervertebral Disc Degeneration Via the TNF-α/NF-κB Pathway: An Integrated Analysis of Single-Cell RNA-Seq, Bulk RNA-Seq, and In Vitro Validation.

PMID 41511606 · PMC12995935 · Applied biochemistry and biotechnology · 2026 · 8 claims · 8 setups

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TEAD4 and RXRA play critical roles in IDD progression, likely regulating NP cell behavior and ECM metabolism via the TNF-α/NF-κB pathway

differential il-1β-induced scrna-seq bulk gsea
sCellST predicts single-cell gene expression from H& E images.

PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

ovarian kidney prostate breast simulation spot-level nucleus
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
Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy.

PMID 41530481 · PMC12877007 · Scientific reports · 2026 · 7 claims · 8 setups

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71 genes show concordant (same-direction) expression changes and 94 genes show concordant methylation changes across both the kindling and kainic acid epilepsy models

hippocampus sequencing reduced-representation rt-pcr
The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

PMID 11178241 · PMC138858 · Genome biology · 2000 · 8 claims · 4 setups

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The V. cholerae O1 (El Tor) genome consists of two chromosomes with asymmetrically distributed gene functions

vibrio whole-genome microarray expression
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.

PMID 18179696 · PMC2231339 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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AGML 2.0 is a comprehensive XML representation for 2-DE experiments comprising identification, protocol (MI2DG), and gel sections

general gel excised clinical 2-dimensional differential mass
The VIZIER project: preparedness against pathogenic RNA viruses.

PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

viruses virus coli soluble large-scale bioinformatic recombinant
Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.

PMID 38352867 · PMC10861739 · Frontiers in immunology · 2024 · 6 claims · 3 setups

Has reproduction · 73

A targeted panel of 176 transcripts plus 8 housekeeping genes was identified for monitoring immunological changes during pregnancy

blood bulk microarray bloodgen3
B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

ebv-transformed cloned rt-pcr southern sequence

Experiments

Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells.

Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.

Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.

Eduomics: a Nextflow pipeline to simulate -omics data for education.

Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.

STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.

Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A.

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation.

TEAD4 and RXRA Regulate the Function of Nucleus Pulposus Cells in Intervertebral Disc Degeneration Via the TNF-α/NF-κB Pathway: An Integrated Analysis of Single-Cell RNA-Seq, Bulk RNA-Seq, and In Vitro Validation.

sCellST predicts single-cell gene expression from H& E images.

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

Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy.

The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.

The VIZIER project: preparedness against pathogenic RNA viruses.

Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.

B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.