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).

• Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

  PMID 29221171 · PMC5707065 · Oncotarget · 2017 · 8 claims · 6 setups

  Has reproduction · 73

  A customised SAAV peptide database built from RNA-seq/WGS variant calls can be used to search proteomics data and detect single amino acid variant (SAAV)-containing peptides at the protein level

  jurkat rna-seq genome proteomics

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells represent largely distinct, non-overlapping populations across murine and human aging tissues

  hippocampus brain skeletal bone scrna-seq cytof velocity

• NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution.

  PMID 31156037 · PMC6693550 · RNA biology · 2019 · 8 claims · 7 setups

  Has reproduction · 67

  NET-prism, an adapted NET-seq protocol using immunoprecipitation of Pol II-associated factors, enables strand-specific, nucleotide-resolution interrogation of transcription dynamics for any Pol II-interacting protein.

  e14 mass western net-prism

• Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

  PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

  ucec ishikawa rna-seq proteomics immunohistochemistry

• The mouse gastric surface epithelial cell and its response to early Helicobacter pylori infection.

  PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 6 setups

  Has reproduction · 100

  SMCs show high gene expression for mucus-secreted proteins (Tff1, Gkn1, Gkn2, Psca, Muc5ac), mitoribosome RNA, and cytoskeleton proteins

  laser-microdissected gastric ffpe oct-embedded sequencing glycomics immunofluorescence

• Phosphorylation of SF3B1 by CDK11 orchestrates spliceosome activation via SNIP1-dependent RES complex recruitment.

  PMID 41904131 · PMC13194972 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  CDK11 inhibitor OTS964 traps the spliceosome in a previously uncharacterized intermediate (B_OTS964) that has the NTR complex integrated but the NTC complex not yet associated.

  hct116 gst-sf3b1 ip-mass subcellular iclip-seq

• Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

  PMID 41484081 · PMC12858953 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Combined low-dose CTX + anti-CSF-1R (SNDX-ms6352) is highly effective against aggressive metastatic Trp53-null TNBC models with high macrophage infiltration, producing complete tumor regression in claudin-low models.

  trp53-null complete t12 cell-deficient imaging survival tumor

• Aged murine bone marrow myeloid and mesenchymal cells develop unique senescence phenotypes.

  PMID 41592025 · PMC13038201 · The Journal of clinical investigation · 2026 · 7 claims · 8 setups

  Full-text index only

  Myeloid-lineage cells (monocytes, macrophages, myeloid progenitors) show the highest expression of p16 and SASP markers among bone marrow immune cell types in aged mice

  bone femur skeletal single-cell mass cytof

• Dextrorotatory kynurenine suppresses acute rejection through inhibiting M1 macrophage-mediated inflammation.

  PMID 41644740 · PMC12988155 · EMBO molecular medicine · 2026 · 8 claims · 7 setups

  Full-text index only

  Elevated serum D-Kyn levels correlate with stable graft function, while lower D-Kyn is associated with acute rejection

  serum kidney allogeneic ion scrna-seq pseudotime

• Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

  PMID 33402206 · PMC7784341 · Genome biology · 2021 · 8 claims · 6 setups

  Has reproduction · 74

  Disome-seq detects widespread, previously hidden ribosome collisions across endogenous coding sequences in fast-proliferating yeast cells.

  exponentially yeast sucrose disome-seq cryo-electron

• Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

  PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups

  Has reproduction · 80

  928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase

  burkholderia pseudomallei bulk tmt-based rt-qpcr

• Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).

  PMID 41745774 · PMC12945099 · Toxins · 2026 · 8 claims · 4 setups

  Has reproduction

  Coniophanes DVG transcriptomes contain 18 toxin families, with toxins comprising 38.8% to 66% of total transcriptome expression depending on species

  duvernoy's fissidens venom imperialis rna-seq dicect quantitative

• Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.

  PMID 35508485 · PMC9068813 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  eRNAs longer than 200 nucleotides that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release

  cortical transcribed reconstituted erna-bound gro-seq exo-seq shape-map

• Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

  PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

  Has reproduction · 93

  Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

  huvecs huvec long-read bottom-up offline

• Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

  PMID 37223250 · PMC10117727 · microLife · 2021 · 8 claims · 9 setups

  Has reproduction · 50

  Grad-seq resolves in-gradient sedimentation profiles for ~87-88% of annotated C. difficile transcripts and ~50% of annotated proteins, providing a comprehensive RNA-protein complexome resource

  difficile grad-seq rna-seq lc-ms

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

  PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

  Full-text index only

  JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

  tumor degs cancer jag bulk proteomics gene

• DNA methylation profiles at hospital admission are associated with subsequent severe COVID-19 outcomes.

  PMID 42021404 · PMC13251264 · Clinical epigenetics · 2026 · 7 claims · 5 setups

  Full-text index only

  DNA methylation profiles at hospital admission differ among disease trajectory groups (TGs) and are associated with subsequent disease progression.

  pbmcs blood immune end-stage targeted rna-seq mass

• Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.

  PMID 41539304 · PMC12853167 · Cell reports methods · 2026 · 8 claims · 5 setups

  Full-text index only

  Comprehensive multi-omics reference materials (ATAC-seq, Methyl-seq, RNA-seq, MS-proteomics) were generated for paired HCC1395/HCC1395BL cell lines as a community benchmarking resource

  hcc1395 atac-seq methyl-seq bulk

• A Novel Human Cellular System for Studying Normal Aging and for Anti-Aging Discovery.

  PMID 41556081 · PMC12816977 · Aging cell · 2026 · 6 claims · 8 setups

  Full-text index only

  In vitro hTSC-derived STBs recapitulate in vivo CTB-STB maturation and major cellular aging features, including multinucleation, hormone secretion, cell cycle arrest, genome instability, epigenetic changes, transposable element activation, and SASPs.

  peri-implantation first-trimester term-stage musc scrna-seq bulk linear