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).

• From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

  PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

  Has reproduction · 59

  382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

  semibalanus individual rocky barnacles pool-seq sanger temperature

• Allelotyping of pooled DNA with 250 K SNP microarrays.

  PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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  The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

  pool nspi individual snp individual call

• Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.

  PMID 17142224 · PMC1669776 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Pure (GAA·TTC)44+ alleles at the FXN locus are unstable in human somatic cells in vivo, showing both expansions and contractions.

  blood v34a cos1 cv1 small genome-wide strip

• An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

  PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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  Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

  pooled australian independent trio pool snapshot snplex

• Chemical genomics: what will it take and who gets to play?

  PMID 11423004 · PMC138939 · Genome biology · 2001 · 8 claims · 8 setups

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  Scaling chemical genetics to a genome-wide 'chemical genomics' requires large, well-funded, multidisciplinary centers that integrate compound libraries, protein resources, automation, and profiling technology, and freely distribute data and reagents.

  iccb fluorescently yeast engineered cell-based small-molecule expression

• SNP haplotype tagging from DNA pools of two individuals.

  PMID 12709267 · PMC156884 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  An algorithm can reconstruct haplotypes from pools of two individuals' DNA under very general conditions, without requiring Hardy-Weinberg equilibrium.

  add2 pooling computational exhaustive

• Advances in the study of SR protein family.

  PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

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  SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

  nuclear bovine drosophila caenorhabditis selex rna-binding splicing

• Protocol for assessing regulatory elements in murine heart using an AAV9-based massively parallel reporter assay.

  PMID 40252222 · PMC12033988 · STAR protocols · 2025 · 8 claims · 5 setups

  Has reproduction · 93

  An AAV9-based in vivo MPRA (AAV-MPRA) workflow, combined with a companion informatics platform, can dissect and quantify enhancer activity in mouse heart.

  agilent stbl3 hek293t wild-type self-annealing restriction plasmid

• Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

  PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

  calanus sinicus genomic rna-seq novo sequence

• Early life-stage thermal resilience is determined by climate-linked regulatory variation.

  PMID 41505517 · PMC12799179 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Embryonic heat tolerance in D. melanogaster is determined by climate-linked regulatory genetic variation at loci on chromosomes 2R and X

  melanogaster simulated synthetic wild-collected heat-shock pool-seq drift-only

• Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

  PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting

  normal aneuploid same genomiphi-amplified array-cgh

• Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways.

  PMID 16186129 · PMC1236719 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Targeted pso-TFO genomic crosslinks resolve via genetically separable pathways leading to either base substitutions or deletions.

  cho same uv41 6-tg small sequencing

• Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

  PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups

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  A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

  t-47d agarose chromatin cloning

• Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

  PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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  High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

  genomic normalized simulated tiling-resolution snp oligonucleotide

• Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

  PMID 19057677 · PMC2585813 · PLoS genetics · 2008 · 7 claims · 8 setups

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  Genome-wide siRNA screening identified 92 novel genes that support melanin production in human melanocytes with a low false discovery rate.

  mnt-1 melanocyte melanocytes genome-wide secondary quantitative

• Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation.

  PMID 18778093 · PMC4582942 · Journal of proteome research · 2008 · 6 claims · 4 setups

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  OGE first-dimension fractionation enabled identification of 156 unique CSF proteins compared to 115 identified using SCX fractionation on the same CSF pool

  pooled csf spectra shotgun trypsin peptide

• 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

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.

  huh7.5 host lung chirp-ms chirp-rna-seq sds-page

• Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

  PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups

  Has reproduction · 95

  Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input

  wheat hordeum bulk-segregated interval novo

• Molecular epidemiology of DFNB1 deafness in France.

  PMID 15070423 · PMC385234 · BMC medical genetics · 2004 · 8 claims · 7 setups

  Full-text index only

  35delG remains the most common pathogenic GJB2 mutation in the studied French (Languedoc Roussillon) population despite being less frequent than in other Mediterranean populations

  gjb2 dried genomic deaf dhplc pcr-mediated pcr-dhplc