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).

• 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

  PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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  3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

  brain hbrr topo-cloned tag microarray quantitative

• Genetical genomic determinants of alcohol consumption in rats and humans.

  PMID 19874574 · PMC2777866 · BMC biology · 2009 · 8 claims · 6 setups

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  A genetical genomics approach combining brain gene expression, bQTL, and eQTL analysis in HXB/BXH RI rats identifies candidate genes for alcohol consumption

  hxb naive caucasian two-bottle behavioral brain

• Somatic mutation of epidermal growth factor receptor in a small subset of cutaneous squamous cell carcinoma.

  PMID 19812598 · PMC2825112 · The Journal of investigative dermatology · 2010 · 8 claims · 5 setups

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  EGFR is activated by somatic mutation in a small subset of cutaneous SCC

  archival scc sanger array-based fluorescence

• FISH and SNP-A karyotyping in myelodysplastic syndromes: improving cytogenetic detection of del(5q), monosomy 7, del(7q), trisomy 8 and del(20q).

  PMID 19758696 · PMC2826525 · Leukemia research · 2010 · 7 claims · 4 setups

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  MC, FISH, and SNP-A are complementary techniques whose combined use improves diagnostic yield for detecting del(5q), -7/del(7q), trisomy 8, and del(20q) in MDS

  bone pellets extracted cd3+ metaphase fluorescence snp

• Methods for proteomic analysis of transcription factors.

  PMID 19726046 · PMC2778203 · Journal of chromatography. A · 2009 · 8 claims · 8 setups

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  Systematic oligonucleotide 'trapping' at nM DNA concentrations allows purification of TF-RE complexes in a highly purified state, exploiting the high specific affinity vs. low non-specific affinity of TFs for DNA

  nuclear crude intact partially emsa southwestern systematic

• Brain progranulin expression in GRN-associated frontotemporal lobar degeneration.

  PMID 19649643 · PMC3104467 · Acta neuropathologica · 2010 · 8 claims · 8 setups

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  GRN transcript haploinsufficiency, previously shown in blood-derived cells, does not hold in most brain regions of GRN mutation carriers

  peripheral postmortem hek293 qrt-pcr microarray rt-pcr

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• The future is genome-wide.

  PMID 16934105 · PMC1779592 · Genome biology · 2006 · 8 claims · 8 setups

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  Noncoding SNPs near NRG1 associated with schizophrenia likely act by influencing NRG1 expression level

  schizophrenia myocardial individuals infectious genetic candidate gene

• 6th annual meeting of the Complex Trait Consortium.

  PMID 17906895 · PMC2042027 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 8 claims · 7 setups

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  The NIEHS Perlegen/resequencing project has generated over 8.5 million SNPs from 15 inbred mouse strains but shows a high false-negative discovery rate, with an estimated 45 million SNPs actually present.

  inbred recombinant yeast gallstone genome affymetrix microarray

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

  PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 100

  TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

  hesc hescs long-read short-read rt-pcr

• High resolution array-CGH analysis of single cells.

  PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

  769p hct116 peripheral single array-cgh gel fish

• Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

  PMID 18160415 · PMC2275099 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  HMGB1 is a novel HNF1α-interacting protein identified via a co-IP-MS screening strategy

  hepg2 recombinant co-immunoprecipitation immunofluorescence gst

• Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

  PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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  Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

  placenta five lines huh7 5'-race rt-pcr real-time

• The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

  PMID 17438525 · PMC2669504 · Molecular vision · 2007 · 8 claims · 8 setups

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  NR2E3 LBD fused to a heterologous Gal4 DBD mediates dose-dependent transcriptional repression on Gal4-responsive reporters.

  cos-1 hela luciferase western electrophoretic

• Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

  PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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  GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

  genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• NEIBank: genomics and bioinformatics resources for vision research.

  PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups

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  NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.

  dissected eye retina cdna est serial sequence

• Proposed methods for testing and selecting the ERCC external RNA controls.

  PMID 16266432 · PMC1325234 · BMC genomics · 2005 · 8 claims · 5 setups

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  A consortium-developed, standardized set of external RNA control transcripts can be used to assess technical performance in gene expression assays (microarray and QRT-PCR)

  candidate linearized transcripts pools sequence transcription quality