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 340

Assay: copy-number ✕ Clear

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

Full-text index only

CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines

a498 frozen normal proteomics flow immunohistochemistry
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

Full-text index only

The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr
Comparative genomic analysis of three Leishmania species that cause diverse human disease.

PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

Full-text index only

L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

infantum major braziliensis leishmania whole-genome comparative pcr
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

Full-text index only

The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
Detection of mutations in EGFR in circulating lung-cancer cells.

PMID 18596266 · PMC3551471 · The New England journal of medicine · 2008 · 8 claims · 7 setups

Full-text index only

The CTC-chip microfluidic device isolates CTCs from NSCLC patients in sufficient quantity and purity to permit EGFR mutational analysis

blood archived nsclc plasma microfluidic allele-specific standard
Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

Full-text index only

A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

p53 tumor tumors computational retroviral linker-mediated flow
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

PMID 18257913 · PMC2374708 · Genome biology · 2008 · 8 claims · 7 setups

Full-text index only

The macaque marker order on chromosome 17 represents the ancestral hominoid/mammalian organization

great felis mus rhesus comparative fish duplicon
Analysis of recent segmental duplications in the bovine genome.

PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

Full-text index only

Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

bos bovine genes cattle genome fluorescent repeat
Genome sequence, comparative analysis, and population genetics of the domestic horse.

PMID 19892987 · PMC3785132 · Science (New York, N.Y.) · 2009 · 8 claims · 7 setups

Full-text index only

Produced a high-quality draft genome assembly of the domestic horse (EquCab2.0)

single horse eight twelve genome fish chip-on-chip
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

Full-text index only

Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp
A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.

PMID 41513996 · PMC12872441 · Nature microbiology · 2026 · 8 claims · 7 setups

Full-text index only

The global cellular tRNA pool is not substantially altered during APMV infection, despite the virus encoding its own tRNA genes.

acanthamoeba apmv rna-seq ribo-seq mim-trna-seq
Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus Leishmania hybrid.

PMID 41918820 · PMC13034039 · NAR molecular medicine · 2026 · 7 claims · 8 setups

Full-text index only

An in vitro cross between L. infantum and L. tarentolae produced a viable inter-subgenus hybrid, demonstrating genomic compatibility between highly divergent Leishmania species.

infantum linf-gfp bone bmdms genetic flow morphological
PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.

hek293t pbmcs melanoma bone single-cell infercnv gene
Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.

PMID 41634861 · PMC12955163 · Genome biology · 2026 · 8 claims · 8 setups

Full-text index only

PHap is a new pipeline that enables haplotype-resolved, near-T2T assembly of autopolyploid genomes using only standard HiFi, ONT-UL, and Hi-C sequencing data

autotetraploid parental huashu4 pacbio hi-c illumina
α4 Integrin blockade impairs CD8+ T cell neuroimmune surveillance following SIV infection.

PMID 41734020 · PMC13078879 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

Full-text index only

α4 blockade preserves CD4+ Th1 cell access to brain parenchyma but impairs CD8 effector recruitment, disrupting antiviral control

siv-infected live macaque cd4-δitga4 flow antibody single-cell
Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.

PMID 41862467 · PMC13168514 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

UCASpatial is a novel deconvolution algorithm that uses Shannon entropy-based gene weighting combined with weighted non-negative least squares to estimate cell-type composition from spatial transcriptomics data

simulated colorectal hippocampus ear simulated runtime spatial
Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.

PMID 41925227 · PMC13099265 · The ISME journal · 2026 · 8 claims · 8 setups

Full-text index only

Built a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes) using culturomics and PacBio HiFi metagenomics

giant panda panda-derived pbac pacbio illumina 16s
pmid-42030940

PMID 42030940 · PMC13163216 · 8 claims · 8 setups

Full-text index only

MECP2 mutations induce an early naïve-like transcriptional drift in human ESCs, marked by upregulation of ZFP42/REX1 and other naïve-enriched markers

isogenic undifferentiated 3-month bulk bulk single-cell single-nucleus
Variation resources at UC Santa Cruz.

PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

Full-text index only

The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

chimpanzee affymetrix hapmap perlegen snp fixed linkage
Single-Cell and Spatial Omics: Methods and Applications.

PMID 41953641 · PMC13053676 · MedComm · 2026 · 8 claims · 8 setups

Full-text index only

Single-cell and spatial omics enable high-resolution molecular profiling that overcomes key limitations of bulk sequencing, revealing cellular heterogeneity and spatial organization central to development, homeostasis, and disease.

a549 hela single dissociated single-cell sc-psilac

Experiments

CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

Comparative genomic analysis of three Leishmania species that cause diverse human disease.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

Detection of mutations in EGFR in circulating lung-cancer cells.

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

Analysis of recent segmental duplications in the bovine genome.

Genome sequence, comparative analysis, and population genetics of the domestic horse.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.

Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus Leishmania hybrid.

PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.

α4 Integrin blockade impairs CD8+ T cell neuroimmune surveillance following SIV infection.

Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.

Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.

pmid-42030940

Variation resources at UC Santa Cruz.

Single-Cell and Spatial Omics: Methods and Applications.