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 29

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

Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

Has reproduction · 75

Endothelial cell-specific deletion of Adgrl2 impairs cerebrovascular integrity in mice

wild-type cortex brain single-molecule single-cell immunohistochemistry
Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize.

PMID 33705553 · PMC8195531 · Plant physiology · 2021 · 8 claims · 4 setups

Has reproduction · 76

Increasing maximum daily temperature (MDT) elevates the frequency of alternative splicing in maize leaves, particularly intron retention (IR) and exon skipping (ES).

maize rna-seq gene differential
scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.

PMID 42085187 · PMC13157062 · STAR protocols · 2026 · 8 claims · 6 setups

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scPASU is a Snakemake-based workflow that quantifies APA from standard 3′ scRNA-seq data without requiring specialized library preparation

ureter processed scrna-seq read poly
Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

Has reproduction · 84

Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

elegans short-read whole-animal rt-pcr
Transcriptome assemblies for two drug-type cannabis chemotypes by long-read RNA sequencing.

PMID 41968651 · PMC13071343 · The plant genome · 2026 · 8 claims · 7 setups

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PacBio Iso-Seq transcriptome assemblies were generated for two contrasting drug-type cannabis chemotypes (THC-dominant and CBD-dominant)

cannabis same pacbio short-read functional
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

full-length alternative refseq genome pairwise mitochondrial signal
Alternative splicing dynamics during human cardiac development in vivo and in vitro.

PMID 41483812 · PMC12925949 · Stem cell reports · 2026 · 8 claims · 8 setups

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iPSC-CMs globally resemble prenatal cardiac cells at both the transcriptional and splicing levels

ipsc-cms heart bulk ipsc-cm immunofluorescence single-cell bulk
A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome.

PMID 41884004 · PMC13010111 · iScience · 2026 · 8 claims · 8 setups

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Malignant cells cluster predominantly by tumor of origin, while non-malignant cells from the same tumors cluster by cell type independent of patient

malignant non-malignant ovarian normal scrna-seq alternative paired
Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.

PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 7 claims · 7 setups

Has reproduction · 50

sctRNA-seq datasets (particularly LCM-seq) show measurable off-target mRNA contamination from surrounding cell types

brain neocortex cortex allen lcm-seq scrna-seq marker
A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

PMID 11476670 · PMC35353 · BMC genetics · 2001 · 8 claims · 7 setups

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The Q279R missense mutation acts as a splicing mutation in vivo, causing skipping of exon 9 (alone or with exon 8) rather than simply altering the encoded amino acid.

microdissected resected non-tumor liver pcr-rflp immunohistochemistry western
Decoding unchanged transcriptome of Alzheimer's disease reveals an NCAM1 mRNA switch as a potential biomarker.

PMID 42006342 · PMC13090632 · iScience · 2026 · 8 claims · 7 setups

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Most genes are gene-level non-differentially expressed (nDEGs) in AD but nDEGs are strongly associated with neuronal function pathways

hippocampus brain bulk alternative isoform
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

Has reproduction · 70

AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr
Protocol for the generation of single-nuclei RNA-seq libraries and quantification of heterogeneous cell types activated during social interaction.

PMID 39423127 · PMC11532268 · STAR protocols · 2024 · 7 claims · 5 setups

Has reproduction · 78

A protocol for dissecting mouse PFC, hippocampus, and cerebellum and generating snRNA-seq libraries can identify neuronal populations activated during social interaction.

medial hippocampus cerebellum brain single-nuclei nuclei bulk
Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.

PMID 41637188 · PMC12932927 · Cell reports · 2026 · 8 claims · 8 setups

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Combined MPRA enhancer assays, RNA-seq (DE/ATU) analysis, and CRISPR-Cas9 engineering to dissect the function of 94 rare non-coding variants (RNVs) associated with blood traits

k-562 chrf-288-11 hl-60 thp-1 massively bulk crispr-cas9
Visualizing the genome: techniques for presenting human genome data and annotations.

PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

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Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation
Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.

PMID 17010193 · PMC1599749 · BMC cancer · 2006 · 8 claims · 4 setups

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No germline deleterious mutations were identified in the ATR coding region among 54 non-BRCA1/2 high-risk French Canadian breast cancer cases.

genomic ebv-transformed normal direct linkage rt-pcr
Transcription and potential functions of a novel XIST isoform in male peripheral glia.

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

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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
Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact
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
Preselection of cases through expert clinical and radiological review significantly increases mutation detection rate in multiple epiphyseal dysplasia.

PMID 17133256 · PMC2670452 · European journal of human genetics : EJHG · 2007 · 7 claims · 3 setups

Full-text index only

Expert clinical-radiological preselection significantly increases mutation detection rate in MED

patients genomic single clinical pcr

Experiments

Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize.

scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.

Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

Transcriptome assemblies for two drug-type cannabis chemotypes by long-read RNA sequencing.

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

Alternative splicing dynamics during human cardiac development in vivo and in vitro.

A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome.

Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.

A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

Decoding unchanged transcriptome of Alzheimer's disease reveals an NCAM1 mRNA switch as a potential biomarker.

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

Protocol for the generation of single-nuclei RNA-seq libraries and quantification of heterogeneous cell types activated during social interaction.

Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.

Visualizing the genome: techniques for presenting human genome data and annotations.

Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.

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

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

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

Preselection of cases through expert clinical and radiological review significantly increases mutation detection rate in multiple epiphyseal dysplasia.