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).

• Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

  PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups

  Has reproduction · 75

  Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.

  testes normal gene rna-seq sapas cdna

• 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

• 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

• 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

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• 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

• Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

  PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups

  Has reproduction · 97

  The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)

  duvernoy's nigriceps rna-seq differential extraction

• Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

  PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

  aeruginosa differentially paired rna-seq tn-seq computational

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

  PMID 34927097 · PMC8649395 · STAR protocols · 2021 · 5 claims · 7 setups

  Has reproduction · 50

  A protocol combining mechanical and enzymatic dissociation of mouse pancreatic tumor yields a single-cell suspension with preserved cell characteristics suitable for single-cell RNA sequencing.

  kpc pancreatic scrna-seq tumor magnetic cd45+

• Structure of the intergenic spacers in chicken ribosomal DNA.

  PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups

  Has reproduction · 80

  Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.

  wag137g04 pacbio gallus_gallus-5.0 chicken long-read novo comparative

• Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection.

  PMID 34145026 · PMC8321655 · Life science alliance · 2021 · 6 claims · 6 setups

  Has reproduction · 54

  ATAC-seq reveals unique neutrophil chromatin accessibility changes in response to different stimuli before transcriptional activation, with most differential regions being challenge-specific in position, function, and motif.

  neutrophils blood healthy atac-seq rna-seq genome-wide

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

  PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 70

  AR enhancer/chromatin binding usage is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites shared by half of tumors analyzed.

  prostate normal ar+ pca chip-seq rna-seq massively

• Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

  PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups

  Has reproduction · 68

  Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.

  cerevisiae colony-forming-unit bulk pooled

• 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 · 6 claims · 6 setups

  Has reproduction · 68

  Phylogenetic analyses of full mitochondrial gene sets recover siphonophores as the first diverging clade within Hydroidolina, a well-supported Leptothecata–Filifera III–IV clade, and a second clade of Aplanulata–Capitata s.s.–Filifera I–II.

  hydrozoan nanomia liriope concatenated long-range rna-seq dna-seq

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups

  Has reproduction · 59

  Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.

  metastatic tcga-brca homo gse40622 gene bulk rt-pcr

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

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

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

  Has reproduction · 87

  Translation strongly affects mRNA stability in a codon-dependent manner in human cells, with specific codons stabilizing or destabilizing mRNAs.

  293t incl endogenous time-course orfome slam-seq

• ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

  PMID 41820617 · PMC13084044 · The EMBO journal · 2026 · 8 claims · 7 setups

  Has reproduction · 50

  ZAP (ZC3HAV1/PARP13) is a key component of the RAPP quality control pathway

  k562 zap-s rt-qpcr western immunofluorescence