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

• The SARS-CoV-2 subgenome landscape and its novel regulatory features.

  PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

  vero caco-2 sars-cov-2 ngs nanopore northern

• Gene expression study on peripheral blood identifies progranulin mutations.

  PMID 18551524 · PMC2773201 · Annals of neurology · 2008 · 7 claims · 3 setups

  Full-text index only

  PGRN is highly expressed in peripheral blood (97th percentile of all array genes)

  peripheral blood-derived microarray direct real-time

• 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

• Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

  PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

  Has reproduction · 50

  Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

  sars-cov-2 publicly simulated simulated amplicon-based variant

• Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.

  PMID 36057548 · PMC9441065 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 6 setups

  Has reproduction · 90

  Commercially available bovine arrays are ineffective at capturing variants segregating among African indicine animals, with only 6% of high-LD (r2>0.8) variants captured by the best arrays versus 17% in African taurine and 25% in European taurine.

  global ndama target illumina whole-genome array genotype

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid