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).

• comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

  PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups

  Has reproduction · 65

  comBO is a single iPSC-derived organoid differentiation that generates osteolineage, vascular, lymphoid, and myeloid compartments together

  hipsc-derived combo combo-derived healthy-donor flow single-cell confocal

• Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils.

  PMID 33948572 · PMC8080108 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 35

  Neutrophils recruited to CF airways undergo rapid, broad transcriptional firing that upregulates anabolic genes and downregulates antimicrobial genes

  blood healthy transmigrated cfasn-transmigrated flow transmigration content

• CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

  PMID 36304334 · PMC9580850 · Frontiers in bioinformatics · 2022 · 8 claims · 5 setups

  Has reproduction · 88

  CIRCprimerXL is a high-throughput, user-friendly circRNA RT-qPCR primer design pipeline available as both a web tool and a standalone Nextflow/Docker pipeline

  synthetic sw480 circrnas rt-qpcr circrna primer

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

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

  Full-text index only

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

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

• Chimeric brain models to study human glial-neuronal and macroglial-microglial interactions.

  PMID 41499239 · PMC12974579 · Cell reports · 2026 · 8 claims · 8 setups

  Full-text index only

  Co-transplantation of pNPCs and PMPs into neonatal mouse brain generates chimeric brains (hMAN) containing human microglia, astroglia, oligodendroglia, and neurons

  hipsc chimeric hpsc-derived flow sequencing immunohistochemistry

• Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament.

  PMID 41587266 · PMC13011956 · The Journal of bone and joint surgery. American volume · 2026 · 8 claims · 5 setups

  Full-text index only

  ACL tissue is heterogeneous, containing 5 major cell types: fibroblasts, pericytes, endothelial cells, macrophages, and T cells.

  acl differentially study flow single-cell immunofluorescence

• The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

  PMID 41686183 · PMC12988592 · Cancer immunology research · 2026 · 7 claims · 7 setups

  Full-text index only

  CD79A is a reliable transcriptomic/protein quantifier of B lymphocytes across differentiation stages, unlike CD19/CD20 whose expression changes upon activation

  healthy tcga luad til-b flow bulk single-cell

• Regulatory-like FOXP3+Helios+CD4+ T conventional cells correlate with T-cell activation after Orca-T immunotherapy.

  PMID 41758930 · PMC13197979 · Blood · 2026 · 8 claims · 6 setups

  Full-text index only

  Orca-T immunotherapy leads to increased phenotypic T-cell activation compared with unmanipulated PBSC grafts, persisting for months after treatment.

  peripheral sorted fresh cryopreserved flow single-cell tcr

• Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

  PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

  Full-text index only

  A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

  tcga-blca blca paired wgcna differential machine

• Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy.

  PMID 33723257 · PMC7961017 · Nature communications · 2021 · 7 claims · 7 setups

  Has reproduction · 70

  Proportions of activated and proliferating CD8+ T cells (cluster C16/activated EM) are significantly higher in responders before and during therapy

  pbmc cd3+cd8+ pbmc-derived metastatic high-dimensional single-cell polychromatic

• Curation of over 10 000 transcriptomic studies to enable data reuse.

  PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups

  Has reproduction · 80

  Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse

  microarray curated geo microarray rna-sequencing probe-to-gene

• Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104).

  PMID 38897205 · PMC11293361 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 72

  Neoadjuvant sintilimab plus carboplatin/nab-paclitaxel is clinically feasible and tolerable in resectable EGFR-mutant NSCLC, with all 18 patients completing treatment and undergoing radical surgery.

  pre resected tumor serial whole-exome bulk single-cell

• Qualitative Transcriptional Signature for the Pathological Diagnosis of Pancreatic Cancer.

  PMID 33173782 · PMC7538791 · Frontiers in molecular biosciences · 2020 · 8 claims · 7 setups

  Has reproduction · 71

  A 12-gene-pair (17-gene) REO-based signature discriminates PC and cancer-adjacent normal tissue from non-tumor (healthy/pancreatitis) pancreatic tissue.

  pancreatic normal pooled microarray rna-sequencing roc

• Why an integrated view of gene expression studies on hematopoiesis in mouse aging is better than the sum of their parts.

  PMID 38627103 · PMC11586588 · FEBS letters · 2024 · 7 claims · 4 setups

  Has reproduction · 75

  Combining differentially expressed (DE) gene lists from multiple publications into a unified 'aging list' (AL) with citation counts, and deriving a shorter high-confidence 'aging signature' (AS, genes cited in >3 publications, ~200 genes), produces a more reliable and consistent picture of hematopoietic aging than any single study.

  hematopoietic compiled gene bulk single-cell

• SGCP: a spectral self-learning method for clustering genes in co-expression networks.

  PMID 38956463 · PMC11221046 · BMC bioinformatics · 2024 · 7 claims · 4 setups

  Has reproduction · 51

  SGCP, a spectral self-learning method, yields gene co-expression modules with higher GO enrichment than WGCNA, CoExpNets, and CEMiTool across 12 real gene expression datasets.

  real microarray rna-seq same gene dna-microarray rna-sequencing

• Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

  PMID 33690630 · PMC7978347 · PLoS genetics · 2021 · 8 claims · 4 setups

  Has reproduction · 97

  Paramutation between R and S HPT epialleles occurs only in tetraploid (RRSS) F2 progeny, not in diploid (RS) F2 progeny, reducing the ratio of hygromycin-resistant plants below Mendelian expectation.

  diploid 14-day-old tetraploid type hygromycin small crispr-cas9

• 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

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.

  PMID 36107487 · PMC9534548 · eLife · 2022 · 8 claims · 8 setups

  Full-text index only

  Colorectal cancer (CRC) cells are coupled by gap junctions assembled predominantly from Cx26 (GJB2)

  colorectal normal crc microarray tcga single-cell

• Genomic and Immune Landscape of Recurrent and/or Metastatic Squamous Cell Carcinoma of the Head and Neck Progressing on Anti-PD-1 Treatment.

  PMID 41666253 · PMC13044521 · Cancer immunology research · 2026 · 6 claims · 8 setups

  Full-text index only

  Tumor biopsies from anti-PD-1-resistant SCCHN show significantly more EGFR and MYCL amplifications and increased MYC pathway alterations compared with anti-PD-1-naive tumors

  ffpe blood tumor whole-exome bulk multiplex