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 22

System / cell line: single ✕ Assay: transfection ✕ Clear

Autocrine SFRP2 (secreted frizzled related protein 2) enhances lung myofibroblast fibrogenic activity by suppressing PINK1-mediated mitophagy initiation.

PMID 41789512 · PMC13185440 · Autophagy · 2026 · 7 claims · 8 setups

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SFRP2 is specifically highly expressed in myofibroblasts derived from fibrotic (IPF/BLM/TGFB1-induced) lung tissue

lung pmlfs mrc5 single-cell bulk histology
TBP regulates transposable element expression in early mouse embryos.

PMID 41862641 · PMC13144441 · The EMBO journal · 2026 · 8 claims · 6 setups

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The general transcription factor TBP binds and activates MaLR transposable elements in mouse embryos

single embryos computational embryonic rna-seq atac-seq motif
Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

PMID 18616294 · PMC2646719 · Biochemistry · 2008 · 8 claims · 6 setups

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Both G[8,5-Me]T and T[5-Me,8]G intrastrand cross-links are strongly mutagenic in COS-7 and 293T mammalian cells

cos-7 293t synthetic pms2 shuttle primer steady-state
Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

urothelial urothelial-specific ureter hek293t single-cell poly fluorescence
Insights from pooled CRISPRi single-cell screens in K562 cells reveal gene functions, regulatory networks, and highlight opportunities and limitations.

PMID 41826830 · PMC13097927 · BMC genomics · 2026 · 7 claims · 7 setups

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A modified CROP-seq-CRISPRi protocol allows direct capture of sgRNAs from the cDNA library without a separate enrichment step, improving sgRNA assignment per cell

k562 lentiviral pooled plasmid amplicon
Spatial perturb-seq: single-cell functional genomics within intact tissue architecture.

PMID 41723140 · PMC13035813 · Nature communications · 2026 · 8 claims · 8 setups

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Spatial Perturb-Seq simultaneously measures whole transcriptome (cell type), CRISPR barcodes (perturbation), spatial coordinates, and cell-cell interactions through a single Stereo-seq and/or Xenium run.

hippocampus bone brain aav-transduced scrna-seq snrna-seq spatial
Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

magi pbmc 293t supt1 sensitive rt-pcr western
In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

PMID 17726045 · PMC2094079 · Nucleic acids research · 2007 · 8 claims · 6 setups

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Two exonic mutations, PINK1 E417G and PARK7 E64D, disrupt binding to U1 snRNA and cause skipping of the mutation-harboring exon

hek293 genome lymphocytes minigene artificial genome-wide
Novel approaches for identifying target antigens of autoreactive human B and T cells.

PMID 19763575 · PMC2845891 · Seminars in immunopathology · 2009 · 8 claims · 8 setups

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CD8+ T cells infiltrating MS brain and IM muscle tissue show clonal expansions consistent with antigen-driven selection

muscle brain morphologically autopsy cdr3-spectratyping single-cell immunohistochemistry
Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups

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The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes

schistosoma brugia ancylostoma echinococcus whole-genome interference transgenesis
Synthetic super-enhancers enable precision viral immunotherapy.

PMID 41951744 · PMC13149004 · Nature · 2026 · 8 claims · 8 setups

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Synthetic super-enhancers (SSEs) assembled from validated 160 bp SOX2/SOX9-bound enhancer fragments achieve strong and highly selective transcriptional activity in glioblastoma stem cells (GSCs)

gsc7 patient-derived seven id2904 luciferase flow chip-seq
Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

PMID 19698114 · PMC2749045 · BMC infectious diseases · 2009 · 8 claims · 7 setups

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Three PRNP mutations—D178N, E200K, and M232R—were identified in heterozygosity in Korean probable CJD patients, marking their first report in this population.

csf 293t genomic pcr western recombinant sequencing
Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

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Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

liver hepg2 293t serum bulk single-cell oil
Integrative Multiomic Classification Reveals Distinct Origins and Evolutionary Trajectories of Thymic Epithelial Tumors.

PMID 41671387 · PMC13012242 · Cancer research · 2026 · 8 claims · 8 setups

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TETs stratify into three molecular subgroups with distinct origins: GTF2I-type thymomas, CN-type thymomas, and thymic carcinomas

tet thymic hek293t whole-exome whole-genome bulk
The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos.

PMID 41917015 · PMC13201599 · Nature communications · 2026 · 8 claims · 8 setups

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eccDNA is widespread in mouse preimplantation embryos across all six developmental stages examined

ivf-derived 2-cell preimplantation fibroblasts mda-based reverse chip-seq
Translating genome sequences into biological understanding.

PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups

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Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.

embryonic transfectable drosophila computational gene-trap pooled cross-species
Identification of a dominant epitope of glutamic acid decarboxylase (GAD-65) recognized by autoantibodies in stiff-man syndrome.

PMID 8245784 · PMC2191306 · The Journal of experimental medicine · 1993 · 8 claims · 6 setups

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All 30 SMS patient sera selectively recognize GAD-65, but not GAD-67, when tested by Western blotting on denatured GAD.

brain bacterial triton cho western immunoprecipitation immunocytochemistry
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
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
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

Experiments

Autocrine SFRP2 (secreted frizzled related protein 2) enhances lung myofibroblast fibrogenic activity by suppressing PINK1-mediated mitophagy initiation.

TBP regulates transposable element expression in early mouse embryos.

Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

Insights from pooled CRISPRi single-cell screens in K562 cells reveal gene functions, regulatory networks, and highlight opportunities and limitations.

Spatial perturb-seq: single-cell functional genomics within intact tissue architecture.

Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.

Novel approaches for identifying target antigens of autoreactive human B and T cells.

Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

Synthetic super-enhancers enable precision viral immunotherapy.

Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

Integrative Multiomic Classification Reveals Distinct Origins and Evolutionary Trajectories of Thymic Epithelial Tumors.

The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos.

Translating genome sequences into biological understanding.

Identification of a dominant epitope of glutamic acid decarboxylase (GAD-65) recognized by autoantibodies in stiff-man syndrome.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

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

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