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).

• Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

  PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups

  Has reproduction · 85

  Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.

  liver huh-7 bulk sirna lipid

• Long non-coding RNA LINC00607 epigenetically regulates endothelial TSPAN18 to promote hypoxia-induced thromboinflammation.

  PMID 41581880 · PMC12992942 · The Journal of biological chemistry · 2026 · 8 claims · 8 setups

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  LINC00607 is a hypoxia-inducible, endothelial-enriched lncRNA that positively regulates TSPAN18 expression

  huvecs rna-seq gro-seq atac-seq

• Improved reconstruction of transcripts and coding sequences from RNA-seq data.

  PMID 41700087 · PMC12910111 · Nucleic acids research · 2026 · 7 claims · 3 setups

  Full-text index only

  GeMoSeq combines combinatorial enumeration of candidate transcripts, splitting heuristics, and likelihood-based (EM) quantification for transcript reconstruction from RNA-seq data

  arabidopsis nicotiana mapped rna-seq-based combined read

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.

  PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 71

  13,401 lncRNAs were identified in the A. crassicauda transcriptome using the ECF pipeline

  crassicauda rna-seq coding sequence

• CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

  PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

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  CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

  arabidopsis bulk rna-seq-based rna-seq

• lncEvo: automated identification and conservation study of long noncoding RNAs.

  PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 61

  lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.

  chimp assembled pairwise raw bulk lncrna comparative

• miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.

  PMID 32374865 · PMC7319446 · Nucleic acids research · 2020 · 8 claims · 5 setups

  Has reproduction · 61

  miEAA 2.0 extends miRNA enrichment analysis to ten species (previously only Homo sapiens), accepting both precursor and mature miRNA input.

  kidney blood model geo bulk small agilent

• Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons.

  PMID 34194426 · PMC8236716 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Full-text index only

  Genes in the SRP-dependent cotranslational protein targeting to membrane (ER translocation) pathway and ribosomal subunit genes are strongly and specifically enriched for arginine and lysine residues, suggesting high susceptibility to gingipain cleavage.

  protein-coding coli recombinant postmortem proteome-wide gene gingipain

• Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

  PMID 41578372 · PMC12911049 · Biology of sex differences · 2026 · 8 claims · 8 setups

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  48 tumor-specific sex-biased (TSSB) microRNAs were identified in bladder cancer, mostly located on autosomes rather than sex chromosomes

  tcga tssb blca mirna-seq bulk kegg

• Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes.

  PMID 41882679 · PMC13019944 · Genome biology · 2026 · 8 claims · 7 setups

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  The majority of long-range intronic RNA duplexes detected genome-wide are mediated by inverted Alu-repeat elements.

  k562 hek293t chimpanzee computational splash eclip-seq

• Translation affects mRNA stability in a codon-dependent manner in human cells.

  PMID 31012849 · PMC6529216 · eLife · 2019 · 8 claims · 6 setups

  Has reproduction · 87

  Translation affects mRNA stability in a codon-dependent manner in human cells

  293t time-course orfome slam-seq

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 77

  Recurrently targeted HIV-1 integration genes (RIGs) are proximal to super-enhancer (SE) genomic elements

  activated cd4+ cd3 jurkat chip-seq hiv-1 sequencing

• Reactivation of a developmentally silenced embryonic globin gene.

  PMID 34290235 · PMC8295333 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  In embryonic (primitive) erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD of open, acetylated chromatin and physically interacts with the α-globin super-enhancer.

  primitive embryos ζ-venus atac-seq dnasei chip-seq

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

  PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups

  Has reproduction · 69

  Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.

  mus chuniphyes hormiphora pleuromamma rna-seq homology

• Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.

  PMID 41484656 · PMC12857045 · Genome biology · 2026 · 8 claims · 8 setups

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  pRIC-seq, an adaptation of RIC-seq for plants, enables genome-wide mapping of RNA-RNA spatial interactions in diploid and tetraploid cotton

  diploid tetraploid cotton nicotiana pric-seq gro-cap chip-seq

• A chromosome-scale genome assembly of the striped fruit fly Zeugodacus scutellatus (Diptera: Tephritidae).

  PMID 41673002 · PMC13002913 · Scientific data · 2026 · 8 claims · 8 setups

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  A chromosome-scale genome assembly of Z. scutellata was generated using Illumina short reads, PacBio HiFi long reads, and Hi-C scaffolding

  scutellata single assembled whole-genome pacbio hi-c

• EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology.

  PMID 41805684 · PMC12975130 · eLife · 2026 · 8 claims · 8 setups

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  EPB41L4A-AS1 acts in cis to enhance transcription of the proximal EPB41L4A gene

  mcf-7 epb41l4a-as1 rna-seq rt-qpcr single-molecule