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).

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• The HuRef Browser: a web resource for individual human genomics.

  PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.

  individual huref whole-genome assembly-to-assembly variant

• Microglia cause HIV-induced transcriptional and metabolic changes in human neural organoids.

  PMID 41857366 · PMC13021996 · Communications biology · 2026 · 8 claims · 7 setups

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  Microglia are essential for driving HIV-induced transcriptional changes and neuroinflammation in neural organoids

  hipsc-derived neural mno supernatant flow elisa immunocytochemistry

• Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR.

  PMID 41771837 · PMC12953643 · Signal transduction and targeted therapy · 2026 · 8 claims · 8 setups

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  KLF15 transcriptional activity shows the most significant change among TFs in pathological cardiomyocytes during progressive hypertrophic remodeling, reflecting less effective repression of disease-associated genes.

  ventricular heart cardiomyocytes cardiomyocyte single-cell rt-qpcr bulk

• ECgene: an alternative splicing database update.

  PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

  nine genome sage cdna genome-based chi-squared sage

• Genome-wide survey of allele-specific splicing in humans.

  PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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  A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

  genome cdna hapmap computational est exon

• Single-cell analysis of signalling and transcriptional responses to type I interferons.

  PMID 41896367 · PMC13172048 · EMBO reports · 2026 · 7 claims · 6 setups

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  Different immune cell types show cell-type-specific patterns of STAT phosphorylation and gene expression changes in response to type I IFN

  freshly pbmcs mass rt-qpcr bulk

• 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

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr

• Bladder tumour-derived somatic TSC1 missense mutations cause loss of function via distinct mechanisms.

  PMID 18397877 · PMC2427143 · Human molecular genetics · 2008 · 8 claims · 8 setups

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  All six somatic TSC1 missense mutations found in bladder tumours cause loss of TSC1 function, but via distinct molecular mechanisms.

  hcv29 lines tsc1 bladder immunoblotting real-time co-immunoprecipitation

• Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

  PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

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  A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

  genomic lca5 lymphocyte affected snp sanger splice

• Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

  PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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  Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

  tissues genomic gtex hgmd long-read variant splice

• Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples.

  PMID 41844163 · PMC13030975 · Cell reports methods · 2026 · 8 claims · 7 setups

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  Cell lysis (CL) nuclei isolation yields substantially more nuclei and less biased immune cell proportions than mechanical separation (MS)

  frozen paxgene cl-derived thawed single-nucleus confocal brightfield

• Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils.

  PMID 33948572 · PMC8080108 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 35

  Neutrophils recruited to CF airways undergo rapid, broad transcriptional firing that upregulates anabolic genes and downregulates antimicrobial genes

  blood healthy transmigrated cfasn-transmigrated flow transmigration content

• Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

  PMID 16855287 · PMC1524908 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Splicing-affecting genomic variations can account for up to 50% of mutations leading to gene dysfunction in some genes

  random trans-acting tpo fibronectin minigene selex cdna

• Detection of alternative splicing: deep sequencing or deep learning?

  PMID 41520225 · PMC12790623 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  Sequence-based deep learning tools (AlphaGenome, SpliceAI, DeepSplice) show potential for initial hypothesis development and as additional filters in standard RNA-seq pipelines, especially when sequencing depth is limited.

  dilated dcm sequence subsampled bulk rna-seq deep

• Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

  PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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  RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

  peripheral patient-parent genomic crebbp karyotyping bac microsatellite

• Vertebrate gene finding from multiple-species alignments using a two-level strategy.

  PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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  DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

  genomic encode entire chromosome multi-species hmm-based classifier

• Modeling splicing outcome by combining 5'ss strength and splicing regulatory elements.

  PMID 35947702 · PMC9410876 · Nucleic acids research · 2022 · 7 claims · 8 setups

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  In silico designed sequences with a priori prescribed HEXplorer splicing regulatory properties can be concatenated to arbitrary length without changing their regulatory properties

  hela proteins fibroblasts cardiovascular massively rt-pcr quantitative

• Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

  PMID 29907695 · PMC6068466 · The EMBO journal · 2018 · 8 claims · 8 setups

  Has reproduction · 46

  B16F1 and B16F10 melanoma subclones functionally exchange EVs in vivo, transferring Cre mRNA cargo detectable via a Cre-LoxP color-switch reporter system

  co-injected b16f1 locally 16.5k intravital cre-loxp rt-pcr