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).

• Genomic approaches to identifying transcriptional regulators of osteoblast differentiation.

  PMID 12844353 · PMC193624 · Genome biology · 2003 · 8 claims · 4 setups

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  Runx2/Cbfa1 and Osterix (Osx) are master controllers of the osteoblastic lineage; loss of either results in complete absence of a mineralized skeleton.

  bone-marrow-derived calvaria osteoblasts uncommitted microarray

• Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.

  PMID 31918046 · PMC6992905 · iScience · 2020 · 8 claims · 8 setups

  Has reproduction · 96

  Data-driven, high-dimensional ML approaches that learn multivariate signatures directly from genome-wide transcriptomic data (no prior gene selection) yield accurate and robust AML classifiers.

  peripheral pbmc datasets hg-u133 gene bulk machine

• Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

  PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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  277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

  umbilical ucb zebrafish microarray fluorescence-activated quantitative

• An integrative genomic and epigenomic approach for the study of transcriptional regulation.

  PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups

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  Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone

  aml computational help chip-chip gene

• Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma.

  PMID 26895470 · PMC4924754 · Oncotarget · 2016 · 8 claims · 4 setups

  Has reproduction · 36

  31 lncRNAs are deregulated in plasma cell dyscrasia tumor samples compared to normal plasma cell controls (19 upregulated, 12 downregulated)

  plasma gene patients proprietary lncrna custom gene

• Recurring mutations found by sequencing an acute myeloid leukemia genome.

  PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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  Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

  aml-m1 tumor bone additional whole-genome snp gene-expression

• Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

  PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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  Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

  pediatric same oligonucleotide quantitative

• A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.

  PMID 34426512 · PMC8415381 · Genome research · 2021 · 8 claims · 8 setups

  Has reproduction · 57

  About 5% of tested PCRP antibodies showed high-confidence cognate-target enrichment in at least one assay and are strong candidates for further validation.

  k562 hct116 subset chip-exo chip-seq western

• Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

  PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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  Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

  nb4 tf1 tracheobronchial moser affymetrix cdna microarray

• The molecular characterization and clinical management of multiple myeloma in the post-genome era.

  PMID 19657360 · PMC3686133 · Leukemia · 2009 · 8 claims · 8 setups

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  GEP identifies distinct molecular subgroups of MM associated with differing clinical features and survival outcomes

  myeloma cd138-immunomagnetically plasma bone-marrow filter-based gene-expression targeted

• T1DBase, a community web-based resource for type 1 diabetes research.

  PMID 15608258 · PMC540049 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  T1DBase is an integrated, open-access web resource that unifies genetic, genomic, and biological data to support type 1 diabetes (T1D) research

  pancreatic t1d tissues nod microarray genetic est-based

• An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations.

  PMID 32425511 · PMC7218276 · Bioinformatics and biology insights · 2020 · 8 claims · 4 setups

  Has reproduction · 84

  An ensemble methodology integrating nonnegative matrix factorization, a gene.score-based gene landscape extraction procedure, and the WebGestalt functional enrichment tool can automatically mine biologically meaningful biomarkers from microarray datasets of different tumor histotypes.

  cafs bone microarray

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray

• The impact of microRNAs on protein output.

  PMID 18668037 · PMC2745094 · Nature · 2008 · 8 claims · 8 setups

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  MicroRNA targeting for protein repression occurs primarily through seed-matched sites (6mer, 7mer-A1, 7mer-m8, 8mer) located in favourable predicted contexts within 3′ UTRs

  hela neutrophils bone mir-223 quantitative blot microarray

• GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

  PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

  transcriptome genome spliced transcripts est genomic splice-orientation