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).

• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

  PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups

  Has reproduction · 74

  An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead

  ipsc-derived same top differentially bulk principal hierarchical

• The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

  PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups

  Has reproduction · 67

  A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.

  facs-isolated fcrls+ sorted app-ps1 nanostring sequencing quantitative

• Cell fixation and preservation for droplet-based single-cell transcriptomics.

  PMID 28526029 · PMC5438562 · BMC biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  Methanol fixation stabilizes and preserves dissociated cells for weeks without compromising single-cell RNA-seq data quality

  hek293 dissociated facs-sorted hek drop-seq bulk trizol

• Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.

  PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 8 setups

  Has reproduction · 30

  Single-cell transcriptomic analysis of GBA-N370S iPSC-derived dopamine neurons identifies a progressive axis of gene expression variation leading to endoplasmic reticulum stress.

  facs-purified ipsc-derived core bulk single-cell facs

• Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

  PMID 34911933 · PMC8674326 · Nature communications · 2021 · 8 claims · 7 setups

  Has reproduction · 79

  Low-grade (Gleason pattern 3) prostate cancer cells share chromatin accessibility features that are lost in high-grade (Gleason pattern 4) tumours

  flash-frozen tcga single differentially single-cell bulk topic

• Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

  PMID 41507195 · PMC12881518 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  A multi-omics strategy combined with TWAS reveals brain-region-specific molecular signatures and striking gene dysregulation concentrated in inhibitory neurons in an FXTAS mouse model.

  brain prefrontal pfc gabaergic bulk single-nuclei immunofluorescent

• Tachykinin signaling defines distinct populations of glia in the enteric nervous system.

  PMID 41512855 · PMC12832054 · Neuron · 2026 · 8 claims · 8 setups

  Full-text index only

  Mucosal and muscularis glia are transcriptionally distinct populations, with mucosal glia resembling microglia and muscularis glia resembling satellite glia/astrocytes

  ileum gfp+ intestinal intestine bulk scrna-seq bayesprism

• Distinct sympathetic projections to brown fat regulate thermogenesis and glucose tolerance.

  PMID 41559445 · PMC12945688 · Nature metabolism · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Distinct sympathetic neuron subpopulations in the stellate ganglion (SG) innervating iBAT parenchyma versus its vasculature mediate separable functions of the depot.

  th-cre awake ibat plasma retrograde chemogenetic indirect

• Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

  PMID 41675057 · PMC12886552 · iScience · 2026 · 8 claims · 6 setups

  Full-text index only

  Grin2b+/C456Y mice show large-scale, age-dependent brain transcriptomic changes, peaking at 4 weeks postnatally

  brain hippocampus neuronal bulk trade gene

• Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.

  PMID 41053409 · PMC12500777 · Cancer metastasis reviews · 2025 · 8 claims · 8 setups

  Has reproduction

  A 12-step CTC-specific scRNA-seq workflow is proposed, spanning enrichment, single-cell sorting, sequencing, data pre-processing and downstream analysis, to overcome methodological inconsistencies in the field.

  ctcs pooled single neuroblastoma scrna-seq multi-omics