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).

• Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts.

  PMID 39959292 · PMC11825298 · Bio-protocol · 2025 · 7 claims · 6 setups

  Has reproduction · 90

  Mapping adapter-trimmed reads first to the pathogen genome recovers more pathogen reads than the traditional host-first mapping approach.

  monocyte-derived raw same trimmed dual fastqc adapter

• Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.

  PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups

  Has reproduction · 68

  A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.

  hek293 coli dual genome-wide western

• AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

  PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

  Full-text index only

  AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

  genome human-mouse genes initio comparative extrinsic

• Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

  PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

  chicken turkey broiler chromosome single fish

• EGASP: the human ENCODE Genome Annotation Assessment Project.

  PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

  encode computational manual rt-pcr

• A sequence-based survey of the complex structural organization of tumor genomes.

  PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups

  Full-text index only

  End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones

  tumors breast bac bt474 bac low-coverage fluorescence

• A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.

  PMID 30332484 · PMC6192621 · PloS one · 2018 · 7 claims · 8 setups

  Has reproduction · 63

  The CGCG element (consensus TCTCGCGAGA) is a conserved 10-bp motif enriched in TATA-less, CpG island-associated promoters of ribosomal protein and housekeeping genes.

  k562 hek293t motif luciferase bidirectional

• A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans.

  PMID 40629379 · PMC12239316 · BMC biology · 2025 · 8 claims · 7 setups

  Has reproduction · 54

  A 14-bp deletion in the KIT gene promoter region is associated with the all-white phenotype in yaks, identified via GWAS

  domestic re-sampled hek293t yak whole-genome pcr dual-luciferase

• Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

  PMID 16179648 · PMC1236720 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  Deeply conserved human-zebrafish non-coding elements are enriched for in vivo cis-acting transcriptional regulatory activity.

  ncbi genes zebrafish comparative annotation gfp

• Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

  PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

  Full-text index only

  Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

  encode genome cdna-to-genome novo comparative

• Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

  PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

  hela protein-free dual-luciferase reporter thermodynamic

• Ensembl 2008.

  PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

  embryonic amniota multi-species individuals automated chip-chip comparative

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

  Full-text index only

  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr

• Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

  PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

  Full-text index only

  The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

  cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

• Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

  PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation

  quiescent satellite regenerating situ atac-seq rna-seq motif

• Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

  PMID 17470265 · PMC1868759 · BMC genomics · 2007 · 8 claims · 6 setups

  Full-text index only

  There is a clear correlation between MLST clonal complex and the distribution of metabolic genes involved in alternative terminal electron acceptor use.

  jejuni ssh panel suppression blastx dot-blot

• In vivo prime editing rescues alternating hemiplegia of childhood in mice.

  PMID 40695277 · PMC12702498 · Cell · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  PE and BE strategies efficiently correct five prevalent ATP1A3 mutations (D801N, E815K, L839P, G947R-A, G947R-C) in HEK293T cells and AHC patient-derived iPSCs, with 43%-90% correction in iPSCs.

  hek293t ahc n2a b6c3.atp1a3 prime circle-seq rhampseq

• Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

  PMID 19727905 · PMC2946578 · Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2010 · 7 claims · 6 setups

  Full-text index only

  Multiple SNPs and haplotypes in FLNB are significantly associated with BMD at lumbar spine, femoral neck, and total hip

  southern same subjects genotype tag taqman dual-energy

• Colocalization and potential interactions of Endozoicomonas and chlamydiae in microbial aggregates of the coral Pocillopora acuta.

  PMID 37196086 · PMC11809670 · Science advances · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  CAMAs are located in the epidermis of the tentacle tips of P. acuta polyps

  pocillopora acuta lcm-isolated whole-mount fish transmission

• Expression profiling of drug response--from genes to pathways.

  PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups

  Full-text index only

  Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.

  blastocyst skin specified cortex pathway two-color microarray