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).

• MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

  PMID 33849057 · PMC8266615 · Nucleic acids research · 2021 · 8 claims · 7 setups

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  MrHAMER yields >1000s of viral genomes per sample at 99.9% accuracy

  psg3.1 transcribed double-stranded mrhamer transcription reverse mrhamer

• Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

  PMID 26618080 · PMC4655093 · PeerJ · 2015 · 8 claims · 8 setups

  Has reproduction · 68

  Siphonophorae is the first diverging clade within Hydroidolina.

  hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq

• nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

  PMID 36961337 · PMC10199315 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 88

  nf-core/isoseq is a new automated Nextflow-based pipeline that processes raw Iso-Seq subreads through to genome annotation (BED format) without requiring transcriptome assembly.

  organism-specific iso-seq reference mapped pacbio subread long-read

• Structure of the intergenic spacers in chicken ribosomal DNA.

  PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 6 setups

  Has reproduction · 80

  Long-read PacBio RSII sequencing of a BAC clone plus HGAP assembly can resolve the complete, highly repetitive chicken IGS structure that short-read (Illumina) sequencing previously failed to assemble.

  bac pacbio gallus_gallus-5.0 assembled long-read genome blast

• N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

  PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

  random reference healthy long-term resequencing quantitative sequence

• LINE-1 Locus Transcription Nucleates Oncogenic Chromatin Architecture.

  PMID 41489510 · PMC13040219 · Cancer discovery · 2026 · 8 claims · 8 setups

  Full-text index only

  LINE-1 RNAs are primarily chromatin-associated nascent transcripts rather than cytosolic mRNAs

  mcf7 cancer qrt-pcr single-molecule chirp-seq

• Cell type differences in human cytomegalovirus transcription and epigenetic regulation with insights into major immediate-early enhancer-promoter control.

  PMID 40758707 · PMC12333995 · PLoS pathogens · 2025 · 8 claims · 7 setups

  Has reproduction · 90

  Six viral promoters (UL5, UL72, EP3, UL57-AS, US16-AS, US30-S) are ≥50-fold more active in D-NT2 than in HFF at 96 h post-infection and are classified as viral long promoters.

  d-nt2 hcmv-infected hcmv pro-seq dff-chip promoter

• Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

  PMID 41253754 · PMC12627582 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 10

  Gli1+ fetal cells are the precursors of postnatal long-lived chondroprogenitors (LLCPs) in the growth plate

  fetal left-cart-p21 gli1-creer cartilage single-nuclei scenic bulk

• BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.

  PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts

  barley pacbio illumina read

• Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.

  PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 75

  Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes

  arabidopsis bulk hierarchical gene

• 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

• Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

  PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

  Has reproduction · 93

  24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

  jatropha geo bulk semi-quantitative quantitative

• Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

  PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

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  Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

  alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic