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 4

System / cell line: novel ✕ Assay: blastx ✕ Clear

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

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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
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

Has reproduction · 61

T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

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Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

bimaculatus prothoracic differentially gbig rna-seq genome differential

Experiments

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

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.