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 computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3' UTR structure to RNA metabolism.

  PMID 37013995 · PMC10164587 · Nucleic acids research · 2023 · 7 claims · 5 setups

  Has reproduction · 72

  Extending computational analysis of hiCLIP data (recovering truncated-linker hybrids, direct proximity ligation hybrids without a linker, and short-loop non-hybrid duplexes) increases identified STAU1 duplexes ~10-fold over the original analysis

  hek293t hela hiclip paris ric-seq

• Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

  PMID 34875090 · PMC8887463 · Nucleic acids research · 2022 · 6 claims · 8 setups

  Has reproduction · 56

  Halo-seq pairs a light-activatable Halo-DBF ligand with Click chemistry to label and purify spatially defined RNA populations in living cells with high spatial specificity (~100 nm radius)

  hela apex-seq proximity dot comparative

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm