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).

• Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

  PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  KYNU expression is decreased in melanoma despite a high KYNU mutation rate in the TCGA database

  tcga-skcm melanoma keratinocytes differential copy methylation

• Evolutionary origins of human apoptosis and genome-stability gene networks.

  PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

  apoptosis fully same orthologous protein-protein comparative orthology

• mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice.

  PMID 19763141 · PMC2909846 · Journal of human genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  The G10398A cybrid shows slower proliferation and delayed cell cycle progression (G1 accumulation, decreased G2/M) compared to wild-type G10398 cybrid

  blood mitochondria g10398a cybrid pcr cybrid spectrophotometric

• Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.

  PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 8 claims · 8 setups

  Has reproduction · 73

  NF1 is highly expressed in cetuximab-sensitive CRC cell lines and minimally expressed in cetuximab-resistant ones

  crc cetuximab-sensitive sirna ffpe western growth colony

• Investigations on a clinically and functionally unusual and novel germline p53 mutation.

  PMID 12085209 · PMC2746598 · British journal of cancer · 2002 · 8 claims · 7 setups

  Full-text index only

  A novel germline 7 base pair insertion in exon 5 of p53 (causing frameshift from codon 161 with a stop at codon 182) was identified in a patient with osteosarcoma at age 22 and choroid plexus papilloma at age 29.

  peripheral yeast saos-2 genomic fasay apoptotic

• An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

  PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

  Full-text index only

  shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

  hepatocellular p53 genomic hepatoma array-based pooled shrna

• Malaria research in the post-genomic era.

  PMID 18843360 · PMC2705782 · Nature · 2008 · 8 claims · 7 setups

  Full-text index only

  Genome-dependent methods can partially substitute for forward genetic approaches that are unavailable or limited in malaria parasites.

  falciparum plasmodium malaria hela comparative two-hybrid proteomics

• Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

  PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

  Full-text index only

  R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

  bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation

• Depletion of HIV reservoir by activation of ISR signaling in resting CD4(+)T cells.

  PMID 36590168 · PMC9800255 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 89

  Activation of ISR/ATF4 signaling (via HA15) reverses HIV latency in Jurkat models of HIV latency (J-Lat A1, 2D10)

  jurkat cd4+ hiv-negative resting flow trypan western

• Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

  PMID 41253754 · PMC12627582 · Nature communications · 2025 · 7 claims · 8 setups

  Has reproduction · 10

  Fetal Gli1+ cells (including cells outside the cartilage) are the precursors of postnatal long-lived chondroprogenitors and give rise to most growth-plate chondrocytes juvenile/adult.

  fetal left-cart-p21moe growth gli1creer single-nuclei bulk cre-based

• Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.

  PMID 35951114 · PMC9372016 · Cellular and molecular life sciences : CMLS · 2022 · 8 claims · 8 setups

  Has reproduction · 98

  Coordinated gene expression patterns across cell types are disrupted and re-organized by mTBI with distinct regional, cellular, and temporal (24-h vs 7-day) specificity.

  hippocampus frontal peripheral cell-type single-cell svm-based ligand-receptor

• Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

  PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

  Full-text index only

  CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

  ctll gene promoter metaphase microarray bioinformatics

• Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

  PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

  Full-text index only

  K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

  a549 western proliferation clonogenic

• A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

  PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

  coad consensus cibersort mcp-counter

• CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

  PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

  Full-text index only

  CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

  neuroblastoma nlf athymic methylation-specific quantitative soft