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).

• Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

  PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function.

  PMID 41927596 · PMC13219539 · Nature communications · 2026 · 8 claims · 8 setups

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  Long-read RNA-seq of 72 term placentas yields a high-confidence reference of 37,661 isoforms across 12,302 genes, including thousands of previously unannotated isoforms and genes

  villous placenta tissues placental long-read short-read dnase-seq

• Identification of herpesvirus transcripts from genomic regions around the replication origins.

  PMID 37773348 · PMC10541914 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Herpesviruses display distinct patterns of transcriptional overlaps near or at the replication origins (Oris)

  nine same vzv prv direct cage-seq qrt-pcr

• DDBJ dealing with mass data produced by the second generation sequencer.

  PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.

  plasmodium oryzias gut drosophila solexa wgs metagenomic

• The circadian isoform landscape of mouse livers.

  PMID 41987907 · PMC13076092 · NAR genomics and bioinformatics · 2026 · 5 claims · 6 setups

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  R2C2 long-read nanopore sequencing generates highly accurate, full-length cDNA reads suitable for quantitative detection of circadian oscillations

  c57bl liver r2c2 gene-level short-read

• Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

  PMID 41252442 · PMC12758600 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  Cleanifier is a fast, memory-frugal alignment-free tool for detecting and removing human contamination using gapped k-mers (spaced seeds) and a human pangenome index.

  genomes genome cami t2t host-contamination pangenome

• Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

  PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

  stricta long-read short-read hi-c

• A high-quality chromosome-level genome assembly of a feather star Glyptometra sp. from a deep seamount.

  PMID 41786724 · PMC13079724 · Scientific data · 2026 · 8 claims · 8 setups

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  This is the first chromosome-level genome assembly of a feather star (Glyptometra sp. CNS01629) from a deep seamount

  genomic arm middle assembled k-mer whole-genome pacbio

• Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.

  PMID 41528732 · PMC12958813 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  High-quality de novo genome assemblies were generated for A. andreniformis and A. florea using a hybrid ONT long-read + Illumina short-read sequencing approach.

  andreniformis polished illumina unmasked genomic sequencing genome