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).

• Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.

  PMID 41543530 · PMC12811152 · Microbial genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  HBV splicing efficiency (coSI) correlates more strongly with disease progression than the overall proportion of spliced HBV RNA.

  hbv same host bulk splicing splicebert

• 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

• SpliceHarmonization: an integrated method for identifying RNA splicing events in therapeutics for splicing modulation.

  PMID 41858229 · PMC13064980 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

  Full-text index only

  SpliceHarmonization integrates rMATS, LeafCutter, and MAJIQ outputs into a unified junction-centered format with standardized event type annotations via event graph construction

  sma simulated bulk splicing rt-pcr

• PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

  PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups

  Has reproduction · 90

  PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.

  heart genome rna-seq rt-pcr

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

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

  Full-text index only

  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

• Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).

  PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups

  Has reproduction · 62

  TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR

  potato rna-seq gene alternative

• 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

• Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.

  PMID 34576004 · PMC8466565 · International journal of molecular sciences · 2021 · 8 claims · 8 setups

  Has reproduction · 76

  Both cis- and trans-splicing group II introns in Nymphaea organelle genomes are spliced in random order, generating diverse co-existing intermediates rather than following a fixed splicing sequence.

  nymphaea joey liriodendron pacbio illumina strand-specific

• LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

  PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

  schizosaccharomyces pombe rna-seq lasso lariat-specific

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature.

  PMID 35300606 · PMC8932150 · BMC plant biology · 2022 · 7 claims · 8 setups

  Full-text index only

  Combined SGS+TGS full-length transcriptome sequencing generated 41,016 high-quality potato transcripts, including 15,189 putative new transcripts

  potato pacbio illumina physiological

• SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.

  PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 8 claims · 7 setups

  Has reproduction · 30

  Combined PacBio SMRT and Illumina RNA sequencing generated a full-length reference transcriptome for tall fescue in the absence of a genome sequence.

  tall pooled nicotiana physiological illumina smrt

• Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

  PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups

  Full-text index only

  Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.

  barley extracted tool novel nanopore illumina transcriptome

• Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.

  PMID 41053409 · PMC12500777 · Cancer metastasis reviews · 2025 · 8 claims · 8 setups

  Has reproduction

  A 12-step CTC-specific scRNA-seq workflow is proposed, spanning enrichment, single-cell sorting, sequencing, data pre-processing and downstream analysis, to overcome methodological inconsistencies in the field.

  ctcs pooled single neuroblastoma scrna-seq multi-omics

• Centromere organization and epigenetic regulation in Aristolochia fimbriata.

  PMID 41761339 · PMC13049873 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  A complete gapless telomere-to-telomere (T2T) genome assembly of A. fimbriata was constructed, substantially improving on the previous v1 assembly.

  aristolochia fimbriata pacbio hi-c cenh3

• Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

  PMID 41807385 · PMC12979833 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Integration of CAD GWAS summary statistics with epigenetic data from 45 cell types identifies 1580 candidate CAD genes

  cad-associated disease-relevant types cad variant epigenetic tf-snv

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina