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 Meta-Analysis of the Effects of Acute Sleep Deprivation on the Cortical Transcriptome in Rodent Models.

  PMID 41031900 · PMC13131251 · Journal of sleep research · 2026 · 7 claims · 6 setups

  Has reproduction · 96

  Meta-analysis of 18 SD-vs-control contrasts identified 182 genes differentially expressed in the murine cortex in response to sleep deprivation (FDR < 0.05).

  c57bl full genes meta-analysis affymetrix rna-seq random-effects

• A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence With Existing Human Data.

  PMID 41566898 · PMC12824456 · Brain and behavior · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Chronic stress induces a robust, cross-paradigm PFC transcriptional signature characterized by downregulation of glia/myelin and vascular pathways and suppression of immediate-early gene activity

  c57 c57bl post-weaning pfc microarray rna-seq random

• The seeker R package: simplified fetching and processing of transcriptome data.

  PMID 36389425 · PMC9648347 · PeerJ · 2022 · 8 claims · 4 setups

  Has reproduction · 84

  seeker is an R package that wraps existing tools to fetch and process RNA-seq and microarray data, providing a standard interface, simple parallelization, and detailed logging

  liver microarray rna-seq

• A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors.

  PMID 17090591 · PMC1669715 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  Current ChIP-chip and ChIP-PET technology is sufficient for unambiguous de novo identification of transcription factor binding motifs in mammalian genomes.

  gli oct4 sox2 nanog chip-chip chip-pet

• Transcriptome annotation using tandem SAGE tags.

  PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)

  monocyte-derived unigene genome macrophage sage modified virtual

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage