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).

• Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

  PMID 18281699 · PMC2367731 · Nucleic acids research · 2008 · 8 claims · 7 setups

  Full-text index only

  H3t/H4 forms nucleosomes with H2A/H2B via the salt-dialysis method, similar to conventional H3.1/H4

  recombinant reconstituted his6-tagged hnap1 salt-dialysis micrococcal chaperone-mediated

• Reactivation of a developmentally silenced embryonic globin gene.

  PMID 34290235 · PMC8295333 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  In embryonic (primitive) erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD of open, acetylated chromatin and physically interacts with the α-globin super-enhancer.

  primitive embryos ζ-venus atac-seq dnasei chip-seq

• Comprehensive comparison of gene expression diversity among a variety of human stem cells.

  PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 6 claims · 7 setups

  Has reproduction · 71

  iPSC gene expression is more strongly influenced by tissue origin than other stem cell types, whereas ESCs and somatic stem cells (MSCs, HSCs) are more strongly impacted by culture condition.

  undifferentiated stem batch-corrected bulk microarray batch

• A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

  PMID 18613715 · PMC2601597 · Journal of proteome research · 2008 · 8 claims · 5 setups

  Full-text index only

  A NCI source coupled via an added octopole and the c-trap to a QLT-orbitrap enables fast, efficient ETD reagent anion injection (4-8 ms)

  saccharomyces histone glioblastoma fluoranthene lc-ms etd anion

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

  Full-text index only

  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• Mass spectrometry for proteomics.

  PMID 18718552 · PMC2642903 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

  Full-text index only

  New instrumentation (Orbitrap) and new fragmentation methods (ETD) have enabled exciting new areas of proteomic application

  digested intact yeast large shotgun top-down quantitative

• Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

  PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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  QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

  paired colorectal genome normal quma auma bioinformatic