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).

• A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

  PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

  faecal rsr 16s sargasso shotgun blastn-based 16s

• Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

  PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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  Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

  large-insert patients test genomic array-cgh manual automated

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• Computational comparison of two mouse draft genomes and the human golden path.

  PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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  The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

  newly genome chromosome genomic blat blastn repeat

• IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

  PMID 11056671 · PMC17813 · Arthritis research · 2000 · 8 claims · 5 setups

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  Somatically mutated IgVH genes with amino acid deletions and mixed IgV molecules were found in all three anatomical regions, suggesting a novel pathway for generating (auto)antibody specificities

  synovial same cryosections formalin-fixed cdna seminested double

• A catalog of human cDNA expression clones and its application to structural genomics.

  PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

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  A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

  hex1 ensembl coli recombinant small-scale tag-sequencing blastp

• hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

  PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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  hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

  mgc cloned orfs genome gateway orf blat

• 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

• Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells.

  PMID 19820112 · PMC2808965 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  The Dynamic Proteomics database compiles fluorescence dynamics and localization data for endogenously YFP/Venus-tagged human proteins from the LARC library studied by Cohen et al.

  h1299 cdna user-submitted time-lapse cd-tagging race

• Integration of cytogenetic landmarks into the draft sequence of the human genome.

  PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

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  7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

  large-insert bac ml-2 dgap012 fluorescence sts array

• Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

  PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

  full-length alternative refseq genome pairwise mitochondrial signal

• Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

  PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

  pediatric tumor eight desmoplastic aprimes bisulfite quantitative

• Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

  PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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  A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

  bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow

• Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

  PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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  XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

  hct116 macaque cos-7 genomic cdna est molecular

• Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

  PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

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  Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

  imr-32 subtracted mycn-amplified suppression differential array

• 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

• Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

  PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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  Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

  c57bl orthologous alpha-defensin defensin manual comparative sequence

• Molecular correlates of host specialization in Staphylococcus aureus.

  PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

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  Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

  aureus sequenced et3-1 bovine whole-genome comparative substitution

• Twin peaks: the draft human genome sequence.

  PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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  The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

  genome genomic genes yeast whole-genome bac computational

• Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

  PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

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  Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

  falciparum cdna c18 genomic rt-pcr southern genomic