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).

• Alternative splicing dynamics during human cardiac development in vivo and in vitro.

  PMID 41483812 · PMC12925949 · Stem cell reports · 2026 · 8 claims · 8 setups

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  iPSC-CMs globally resemble prenatal cardiac cells at both the transcriptional and splicing levels

  ipsc-cms heart bulk ipsc-cm immunofluorescence single-cell bulk

• Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.

  PMID 41674383 · PMC12895067 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  HNRNPU forms extensive protein networks including an association with the mammalian SWI/SNF chromatin-remodeling complex

  ipsc-derived computational neocortical ip-ms formaldehyde alphapulldown expression-weighted

• 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

• Mechanical compression induces neuronal apoptosis, reduces synaptic activity, and promotes glial neuroinflammation in mice and humans.

  PMID 41481451 · PMC12773780 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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  Chronic mechanical compression (0.14 kPa) directly induces neuronal apoptosis in human iPSC-derived neurons cocultured with murine glia

  ipsc-derived gfp-expressing mglia astrocytes hoechst gfp+ immunofluorescence

• Genetically engineered stem cell-derived retinal grafts for improved retinal reconstruction after transplantation.

  PMID 34409267 · PMC8361135 · iScience · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Bhlhb4−/− and Islet1−/− pluripotent cell lines differentiate into retinal organoids with similar timing, morphology, and gene expression to wt lines up to around DD15

  bhlhb4− nrl-gfp rd1 fluorescence rt-pcr microarray

• Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases.

  PMID 36936782 · PMC10014280 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 74

  A novel protocol using FGF/EGF/heparin growth factor supplementation and 10% CO2 culture generates cerebral organoids containing neurons, astrocytes, and microglia from iPSCs/hESCs

  hesc-derived hesc als-pdc-affected cerebral microarray immunostaining bulk

• Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.

  PMID 34282405 · PMC8285288 · Frontiers in cellular and infection microbiology · 2021 · 8 claims · 7 setups

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  iPSC-derived pancreatic endocrine and exocrine (acinar/ductal) cultures express ACE2 and TMPRSS2, enabling SARS-CoV-2 entry

  ipsc-derived post-mortem vero-e6 immunofluorescence sars-cov-2 rt-qpcr

• MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.

  PMID 41850290 · PMC13030959 · Cell reports methods · 2026 · 8 claims · 5 setups

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  MASTR-seq couples Cas9-mediated target enrichment, fragment size selection, and PCR-free multiplexed barcoding to increase on-target read proportion and enable pooling of 8-12 samples per Nanopore MinION flow cell

  patient-derived fmr1 hipsc cas9 cas9-mediated pcr hmw

• 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

• Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development.

  PMID 41577697 · PMC12932823 · Nature communications · 2026 · 8 claims · 6 setups

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  DOE-based multifactorial screening combined with bulk RNA-seq comparison to scRNA-seq pharyngeal atlases identifies signaling factors that optimize iPSc differentiation toward thymic epithelial progenitors (TEPs)

  ipsc embryonic ipsc-derived bulk scrna-seq qpcr

• A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data.

  PMID 41484206 · PMC12905373 · EMBO molecular medicine · 2026 · 6 claims · 7 setups

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  INS R6C is a recessive loss-of-function mutation causing diabetes only in homozygous individuals, not a dominant mutation as previously classified.

  blood serum large-scale computational targeted autoantibody population

• Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

  PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 5 setups

  Has reproduction · 94

  EiaD is a reproducible, versioned RNA-seq transcriptome dataset combining 916 healthy human eye samples and 1375 GTEx body samples across 19 eye and 54 body tissues, built with a Snakemake pipeline and served as a single SQLite database.

  gtex eye stem retinal bulk differential single-cell

• Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.

  PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.

  cervical als top yeast bulk stratified protein-protein

• Alternative splicing-triggered mRNA decay informs splice-switching targets for neurodevelopmental disorders.

  PMID 41678398 · PMC13078869 · The Journal of clinical investigation · 2026 · 7 claims · 12 setups

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  EANMD, a new computational tool, identifies AS-NMD exons using the 50 nt rule plus additional transcript-level features and outperforms existing tools (SpliceTools, NMD Classifier)

  neuro2a embryonic e14.5 cortical rna-seq pacbio rt-pcr