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 97

System / cell line: transcription ✕ Assay: type ✕ Clear

MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

PMID 33849057 · PMC8266615 · Nucleic acids research · 2021 · 8 claims · 7 setups

Full-text index only

MrHAMER yields >1000s of viral genomes per sample at 99.9% accuracy

psg3.1 transcribed double-stranded mrhamer transcription reverse mrhamer
Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 8 claims · 6 setups

Has reproduction · 59

Fourteen gene modules were consistently (Bonferroni-corrected) associated with ReHo across a discovery sample and two independent replication samples (including one non-Chinese HCP cohort).

healthy postmortem ahba neocortex resting-state microarray weighted
Transcription dynamics.

PMID 19782025 · PMC6326382 · Molecular cell · 2009 · 8 claims · 8 setups

Full-text index only

Transcription factors locate their sparse specific binding sites via a 3D scanning mechanism combining rapid nuclear diffusion with frequent, very transient (seconds-scale) nonspecific chromatin interactions.

living linker lac glucocorticoid frap single-molecule nucleosome
Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

Has reproduction · 55

Microglia, endothelial cells, and pericytes exhibit the highest IFN-I activity among PD midbrain cell types, with microglia and endothelial cells showing significantly elevated high-IFN-I-scoring proportions in PD versus controls

midbrain single microglia substantia single-cell scenic monocle
Multiomics and deep learning dissect regulatory syntax in human development.

PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

Full-text index only

The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact
Transcription and potential functions of a novel XIST isoform in male peripheral glia.

PMID 41386982 · PMC12863056 · Genome research · 2026 · 8 claims · 8 setups

Full-text index only

XIST is robustly expressed in male peripheral glia, particularly nonmyelinating Schwann cells, across human heart and skeletal muscle tissue.

heart skeletal atlas peripheral scrna-seq aggregated scatac-seq
Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.

PMID 41664139 · PMC12888363 · Molecular horticulture · 2026 · 7 claims · 7 setups

Full-text index only

Red-fleshed and orange-fleshed Guanxi pomelo arose from two independent somatic mutation events from the same white-fleshed wild type

pomelo wild-type rt-qpcr carotenoid genome
Protocol to annotate dendritic cell maturation types in vivo making use of lipid nanoparticle-based approaches.

PMID 41811845 · PMC12994025 · STAR protocols · 2026 · 8 claims · 8 setups

Full-text index only

Different LNP formulations (cargo type, adjuvant presence) can be used to steer DC maturation along a homeostatic-immunogenic spectrum in vivo

lipid linearized transcribed mc38 lnp transcription agarose
Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

Full-text index only

CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

ctll gene promoter metaphase microarray bioinformatics
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

Full-text index only

PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

PMID 19714378 · PMC2854348 · Neurogenetics · 2010 · 8 claims · 5 setups

Full-text index only

A missense mutation (R560Q) in the SPAST gene's ATPase domain causes bovine spinal dysmyelination

cattle bovine coli affinity-purified snp reverse cdna
Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

Full-text index only

DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

coli plasmids plasmid white plasmid sequencing non-b
A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

PMID 20003495 · PMC2802351 · Orphanet journal of rare diseases · 2009 · 8 claims · 7 setups

Full-text index only

A novel FAH gene mutation, c.103G>A (Ala35Thr), causes a mild, atypical form of tyrosinemia type I

fibroblasts liver genomic tnt northern western liver
Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

Full-text index only

Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

postmortem million+ pfc each single-nucleus umap pseudobulk
Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

Has reproduction · 96

A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

gastric gene scrna-seq tcga single-cell wgcna cell-cell
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

Full-text index only

A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

Full-text index only

SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

blood family unrelated subjects snp family-based linkage
Sequencing the regulatory genome.

PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

Full-text index only

Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

interphase nine beta-globin drosophila nuclear digital chip
Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

Full-text index only

A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

genomic hek293 m17 south sscp dual-luciferase pcr-rflp
Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.

PMID 41515103 · PMC12787715 · Plants (Basel, Switzerland) · 2026 · 8 claims · 8 setups

Full-text index only

295 AP2/ERF transcription factor genes were identified and classified in the S. scabra genome

scabra representative hmm rna-seq qpcr

Experiments

MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

Transcription dynamics.

Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

Multiomics and deep learning dissect regulatory syntax in human development.

Transcription and potential functions of a novel XIST isoform in male peripheral glia.

Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.

Protocol to annotate dendritic cell maturation types in vivo making use of lipid nanoparticle-based approaches.

Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

Genetic variation in PARL influences mitochondrial content.

Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

Sequencing the regulatory genome.

Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.