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).

• AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.

  PMID 17135205 · PMC1781224 · Nucleic acids research · 2007 · 7 claims · 3 setups

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  AnimalQTLdb houses publicly available QTL data for multiple livestock species (pig, cattle, chicken) in one comparable database.

  pig cattle blast comparative database

• Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

  PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

  otx sea elegans endo16 windowed reporter comparative

• Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.

  PMID 17557180 · PMC1998882 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 7 claims · 7 setups

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  A BAC transgene containing Prop1 completely rescues the Prop1 mutant (dwarf) phenotype, showing all necessary regulatory elements lie within the BAC

  pig lemur cv-1 b-prop1 bac comparative transient

• Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

  PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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  The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

  sheep bac dot tandem

• 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

• DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

  PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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  A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

  chromosome dog macaque genomic comparative segmental

• Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

  PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups

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  A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.

  sheep genome bac sequence randomization

• Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

  PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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  Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

  hla-homozygous same mhc indel clone-by-clone gene hla

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio

• Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

  PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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  The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

  tlr4 mus chimpanzee baboon genomic coding sequence

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

  PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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  Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

  orthologous random cattle aligned three-way pairwise bac

• Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

  PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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  A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

  bovine pcr-based comparative rt-pcr

• Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

  PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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  Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

  qbl pgf classical ceph bac comparative gene

• Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

  PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

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  The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

  bovine panel agresearch intact random gene northern

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

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

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  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 novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

  PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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  SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

  bac kidney genomic marathon genomic cdna pcr

• Organization and evolution of the Cyp2 gene cluster on mouse chromosome 7, and comparison with the syntenic human cluster.

  PMID 14630516 · PMC1241748 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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  The mouse Cyp2a-t cluster on chromosome 7 contains 22 loci from the same six CYP2 subfamilies (Cyp2a, Cyp2b, Cyp2f, Cyp2g, Cyp2s, Cyp2t) found in the human cluster

  genomic bac nine restriction bac pcr southern

• DNA sequence and analysis of human chromosome 9.

  PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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  The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

  bac chromosome fibres chimpanzee clone-based restriction computational

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence