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).

• The sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

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  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a near-complete de novo goat genome assembly generated from 117x PacBio and 118x Hi-C data, including the first goat Y chromosome scaffold

  saanen goat testicular nine pacbio illumina hi-c

• Blood Pressure Sunday: introducing genomics to the community through family history.

  PMID 15888234 · PMC1327717 · Preventing chronic disease · 2005 · 7 claims · 5 setups

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  Family history is a significant, longstanding risk factor for high blood pressure and can serve as a practical 'genomic tool' for public health given that routine DNA-based risk testing is not yet available.

  family detroit u.s parish readability community national

• Exome sequencing of a multigenerational human pedigree.

  PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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  Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

  genomic eluted captured pcr microarray-based qpcr next-generation

• Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

  PMID 31092189 · PMC6521551 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 7 setups

  Has reproduction · 45

  Graphtyper outperformed GATK and SAMtools in genotype concordance, non-reference sensitivity, and non-reference discrepancy compared to microarray genotypes

  original sire-son whole-genome multi-sample graph-based

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative

• Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

  PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

  tumor each rna-seq whole-genome targeted pcr-based

• Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

  PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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  Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

  poodle dogs y-chromosome blast pcr nested

• Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.

  PMID 32528441 · PMC7262952 · Frontiers in microbiology · 2020 · 8 claims · 5 setups

  Has reproduction · 100

  WGS-derived antibiotic resistance gene (ARG) coverage can be used to predict antimicrobial resistance in Gram-negative bacteria via machine learning

  gram-negative in-house args curated shotgun genome phenotypic

• Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

  PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

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  Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

  unrelated same snps haplotype snp haplotype pairwise

• Genome-wide analysis of subependymomas shows underlying chromosomal copy number changes involving chromosomes 6, 7, 8 and 14 in a proportion of cases.

  PMID 18397339 · PMC2659379 · Brain pathology (Zurich, Switzerland) · 2008 · 8 claims · 2 setups

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  Whole-genome aCGH reveals chromosomal copy number abnormalities in 5 of 12 (42%) subependymoma cases

  subependymoma whole-genome chromosome

• Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics.

  PMID 17331236 · PMC1868942 · Genome biology · 2007 · 8 claims · 8 setups

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  moDCs and KG-1 cells show significant proteomic differences from primary mDCs, particularly in proteins involved in cell growth/maintenance and cell-cell interaction/integrity.

  mdcs mdc freshly peripheral two-dimensional maldi-tof capture

• Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

  PMID 19956714 · PMC2776354 · PloS one · 2009 · 8 claims · 5 setups

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  3,019 CNVs (2,381 autosomal, 638 X chromosome) were identified across 985 Caucasian and 692 Asian individuals using the Affymetrix 500K array

  same caucasian cau autosomal snp copy population

• Performance of mitochondrial DNA mutations detecting early stage cancer.

  PMID 18834532 · PMC2572633 · BMC cancer · 2008 · 8 claims · 6 setups

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  The Affymetrix MitoChip resequencing array is a high-throughput, higher-resolution alternative to capillary sequencing for detecting mtDNA point mutations and heteroplasmy in clinical specimens.

  matched blood mtdna low-quantity mitochondrial capillary str

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

  PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  Endothelial cell-specific deletion of Adgrl2 impairs cerebrovascular integrity in mice

  wild-type cortex brain single-molecule single-cell immunohistochemistry

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat