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).

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• The genome sequence of the Basking Shark, Cetorhinus maximus (Gunnerus, 1765) (Lamniformes: Cetorhinidae).

  PMID 41938266 · PMC13044535 · Wellcome open research · 2026 · 8 claims · 7 setups

  Full-text index only

  The Cetorhinus maximus genome was assembled into two haplotypes with total lengths of 3993.85 Mb (hap1) and 3817.33 Mb (hap2)

  heart pacbio assembled pacbio hi-c rna-seq

• The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.

  PMID 41625985 · PMC12859430 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The Phakellia ventilabrum genome assembly spans 211.92 Mb with 99.97-99.98% scaffolded into 25 chromosomal pseudomolecules

  phakellia pacbio genome microbial pacbio hi-c sequencing

• The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.

  PMID 41913758 · PMC13033139 · Wellcome open research · 2026 · 6 claims · 7 setups

  Full-text index only

  Genome assembly of Anodontia alba (buttercup lucine) with total length 1,862.85 Mb, 99.28% scaffolded into 18 chromosomal pseudomolecules

  anodontia microbial pacbio hi-c sequencing

• The chromosomal genome sequence of the tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).

  PMID 41993727 · PMC13080331 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The Lamellibrachia columna genome assembly spans 879.73 Mb, with 99.96% scaffolded into 15 chromosomal pseudomolecules

  lamellibrachia columna filtered assembled pacbio hi-c sequencing

• The genome sequence of the Acorn Weevil, Curculio glandium (T.Marsham, 1802) (Coleoptera: Curculionidae).

  PMID 42021765 · PMC13096787 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosomally complete genome assembly was produced for Curculio glandium (Acorn Weevil) as part of the Darwin Tree of Life project

  curculio assembled alternate pacbio hi-c sequencing

• The genome sequence of the Short-tailed Blue, Cupido argiades (Pallas, 1771) (Lepidoptera: Lycaenidae).

  PMID 41815329 · PMC12972722 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was produced for a female Cupido argiades specimen, comprising two haplotypes of 445.87 Mb and 384.46 Mb.

  organism pacbio assembled pacbio hi-c rna-seq

• The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.

  PMID 42116832 · PMC13157608 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  Aurelia sp. 4 chromosomal genome assembly has a total length of 462.10 Mb with 99.99% of sequence scaffolded into 21 chromosomal pseudomolecules

  aurelia microbial pacbio hi-c rna-seq

• The genome sequence of Schreibers's Long-fingered Bat, Miniopterus schreibersii (Kuhl, 1817) (Chiroptera: Miniopteridae).

  PMID 42180417 · PMC13197751 · Wellcome open research · 2026 · 8 claims · 7 setups

  Full-text index only

  A chromosome-level genome assembly was produced for Miniopterus schreibersii from a single male individual, comprising two phased haplotypes.

  miniopterus assembled pacbio hi-c rna-seq

• The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.

  PMID 42232316 · PMC13224822 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  A chromosome-level genome assembly was produced for the sponge Rhopaloeides odorabile using the Tree of Life pipeline

  rhopaloeides odorabile-associated odorabile recovered pacbio hi-c sequencing

• The genome sequence of the chocolate mining bee, Andrena scotica Perkins, 1916 (Hymenoptera: Andrenidae).

  PMID 41960580 · PMC13058575 · Wellcome open research · 2026 · 7 claims · 8 setups

  Full-text index only

  A haploid chromosome-level genome assembly was generated for a male Andrena scotica (chocolate mining bee) specimen.

  andrena pacbio hi-c rna-seq

• The genome sequence of Geoffroy's Bat, Myotis emarginatus (Geoffroy, 1806) (Chiroptera: Vespertilionidae).

  PMID 42238844 · PMC13227098 · Wellcome open research · 2026 · 8 claims · 7 setups

  Full-text index only

  A chromosome-level genome assembly was generated for Myotis emarginatus (Geoffroy's Bat) as part of the Darwin Tree of Life Project

  myotis pacbio hi-c rna-seq