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

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

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

  PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 5 setups

  Has reproduction · 100

  LCM followed by RNA-Seq is a feasible methodology for characterizing gastric SMCs and their host response to H. pylori infection in vivo

  c57bl gastric ffpe rna-seq mass immunofluorescence

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

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

  Has reproduction · 50

  p16+ and p21+ senescent cells are largely distinct, non-overlapping populations across murine and human aging tissues, with only rare double-positive cells

  young spleen brain single-cell mass velocity

• Hepatocyte dedifferentiation in 2D culture reveals extensive transcriptomic and proteomic rewiring.

  PMID 41111196 · PMC12506984 · Hepatology communications · 2025 · 8 claims · 4 setups

  Has reproduction · 77

  24 hours of 2D culturing changes >10,000 genes and ~3000 proteins in primary hepatocytes compared with freshly isolated cells, reflecting major transcriptomic and proteomic rewiring.

  c57bl bulk proteomics single-nucleus

• 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

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.

  huh7.5 host lung chirp-ms chirp-rna-seq sds-page

• 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

• 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

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

  peripheral leukocytes plasma degs bulk single-cell plasma

• 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

  This is the first characterization of the venom profiles (transcriptomic and proteomic) of the genus Coniophanes.

  duvernoy's imperialis venom fissidens novo differential quantitative

• RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia.

  PMID 39820365 · PMC11739599 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  RSK1 is a conserved, exploitable therapeutic dependency across MPN and secondary AML

  sorted mpn cd34+ aml bulk targeted mass

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

  PMID 37572656 · PMC10576612 · Immunity · 2023 · 8 claims · 8 setups

  Has reproduction · 68

  Arg1 expression is induced in lung CD4+ T cells during in vivo influenza infection, ranking among the most highly induced genes.

  flow-sorted cd3 lung cd4+ bulk flow western

• 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

• 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

• Dioxin-elicited decrease in cobalamin redirects propionyl-CoA metabolism to the β-oxidation-like pathway resulting in acrylyl-CoA conjugate buildup.

  PMID 35931118 · PMC9418907 · The Journal of biological chemistry · 2022 · 8 claims · 8 setups

  Has reproduction · 73

  TCDD dose-dependently decreases cobalamin (Cbl) levels, compromising MUT activity and redirecting propionyl-CoA metabolism from the canonical Cbl-dependent carboxylation pathway to the alternate Cbl-independent β-oxidation-like pathway.

  liver hepatic intestinal serum targeted untargeted chip-seq

• CD74 deficiency protects against doxorubicin cardiotoxicity through RRM2-mediated regulation of ferroptosis.

  PMID 42180553 · PMC13198236 · Acta pharmaceutica Sinica. B · 2026 · 8 claims · 8 setups

  Has reproduction · 29

  CD74 levels are elevated in plasma of DOX-exposed breast cancer patients and in DOX-challenged mouse hearts and cardiomyocytes

  plasma cd74− cardiomyocytes hearts elisa echocardiography cardiomyocyte

• L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.

  PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups

  Has reproduction · 74

  L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C

  coli growth crystal colony