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).

• MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.

  PMID 41922875 · PMC13095666 · Nature structural & molecular biology · 2026 · 8 claims · 6 setups

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  MitoPerturb-Seq combines pooled CRISPR–Cas9 screening (CROP-seq) with 10x Genomics multiome (scATAC-seq + scRNA-seq) to simultaneously profile mtDNA sequence/copy number/heteroplasmy and the nuclear transcriptome/chromatin accessibility in single heteroplasmic cells

  cas9-expressing heteroplasmic tfam-ko pooled tap-seq hybridization-capture-based

• Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability.

  PMID 41946711 · PMC13233917 · Nature communications · 2026 · 8 claims · 8 setups

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  Single-oocyte full-length (PacBio long-read) isoform sequencing systematically profiles isoform diversity across human (GV, MI, MII) and mouse (GV, GVBD, MI, MII) oocyte maturation stages

  oocytes oocyte pacbio isoform comparative

• Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.

  PMID 41946881 · PMC13057473 · Communications biology · 2026 · 8 claims · 7 setups

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  Bivalent domains have higher GC content and stronger evolutionary conservation than monovalent regions

  embryonic mesc random bivalent chip-seq rna-seq k-mer-based

• STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing sarcoma aggressiveness.

  PMID 41950086 · PMC13079922 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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  STAG2 loss does not globally attenuate EWS-FLI1 activity but reprograms its chromatin binding, redirecting it from short (1-4x) GGAA-repeat sites toward long/multimeric (≥5x) GGAA-repeat microsatellite enhancers

  a673 tc-71 chip-seq immunoblot atac-seq

• Glioblastoma invasion into different organoid hosts reveals cell-intrinsic and proliferative migratory programs.

  PMID 41959666 · PMC13059114 · iScience · 2026 · 8 claims · 8 setups

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  GB cells invade both neural and endodermal organoid hosts (lineage-independent), whereas non-malignant neural progenitor cells show markedly reduced infiltration

  gbm1 gfp-gbm1 facs-sorted post-invasion image-based immunofluorescence single-cell

• High-quality acinar cell isolation enables single-cell analysis of healthy and injured pancreas.

  PMID 42013858 · PMC13198085 · Cell reports methods · 2026 · 8 claims · 7 setups

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  The DCTC protocol isolates up to 90% acinar cells from healthy wild-type pancreatic tissue without cell fixation or dead-cell removal kits

  healthy pancreas epithelial kpc scrna-seq pseudobulk velocity

• A transcriptomic-based model associated with PARP inhibitor sensitivity and immunogenic signatures in ovarian cancer.

  PMID 42014663 · PMC13230468 · Discover oncology · 2026 · 8 claims · 8 setups

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  A 23-gene PARPi-sensor transcriptomic model stratifies ovarian cancer patients into high- and low-risk groups with significantly different overall survival, validated in TCGA and ICGC cohorts

  pdx tcga prognostic tcia bulk non-negative univariate

• Preserved mitochondrial ribosomal protein gene expression marks a youthful transcriptional state in Chinese nonagenarians and centenarians.

  PMID 42030936 · PMC13198318 · Cell reports. Medicine · 2026 · 8 claims · 6 setups

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  LLIs exhibit a transcriptional age younger than expected for their chronological age, as measured by clocks trained on younger controls (YCs).

  peripheral european same age-related bulk gene machine

• Bulk RNA-seq datasets analysis integration identifies robust drought-responsive genes and functional networks in Eucalyptus grandis.

  PMID 42038403 · PMC13106539 · Frontiers in bioinformatics · 2026 · 7 claims · 7 setups

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  Meta-analysis integration of three independent RNA-seq drought studies identifies 472 robust differentially expressed genes (274 up, 198 down) that remain significant across the full meta-analysis and all leave-one-out Jackknife iterations

  grandis computational consistently bulk differential leave-one-out

• Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

  PMID 42050900 · PMC13137916 · Medical science monitor : international medical journal of experimental and clinical research · 2026 · 8 claims · 8 setups

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  TAGs are linked to HGSOC progression and yield a candidate prognostic model

  hgsoc tcga-ov scrna-seq-derived single-cell bulk cellchat

• Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

  PMID 42074506 · PMC13116210 · Genes · 2026 · 7 claims · 8 setups

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  γδT cells in colorectal cancer form five distinct subsets (C0_FCER1G, C1_IL7R, C2_CD81, C3_TOP2A, C4_CXCL13) with distinct marker genes and functional states

  crc γδt epithelial c4_cxcl13 single-cell differential pseudotime

• A Cross-Species Single-Cell Atlas Reveals Conserved Regulatory Networks and Candidate Hearing Loss Genes in the Cochlea.

  PMID 42074555 · PMC13115875 · Genes · 2026 · 8 claims · 8 setups

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  A cross-species single-cell/single-nucleus RNA-seq atlas of human fetal and mouse postnatal cochlea identifies 19 conserved major cell types

  cochlea fetal top scrna-seq snrna-seq cell-cell

• Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons.

  PMID 42102821 · PMC13261877 · Stem cell reports · 2026 · 8 claims · 7 setups

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  Under basal conditions, XDP patient-derived neurons exhibit predominantly upregulated pathways compared to controls

  ipsc-derived rna-seq immunofluorescence bulk rt-pcr

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

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  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative