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).

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 8 claims · 7 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are diverse and abundant in the halite endolithic microbial community, with 1,538 total ncRNAs discovered across Archaea and Bacteria.

  halite discovered conserved itsrnas strand-specific genome-resolved srna

• Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

  PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

  tumor each rna-seq whole-genome targeted pcr-based

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups

  Has reproduction · 67

  A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.

  mammary five singlecellexperiment individual droplet-based quality doublet

• Genomic expression during human myelopoiesis.

  PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

  Full-text index only

  An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

  myeloid same cd34+ gene microarray unsupervised sam

• Age Deceleration and Reversal Gene Patterns in Dauer Diapause.

  PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption

  daf-2 wild-type same dauer developmental lifespan brood

• Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.

  PMID 41767255 · PMC12936829 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 100

  MSI status can be heterogeneous at the single-cell level within a tumor, challenging its use as a binary biomarker

  cancer aggregate single-cell homogeneously single-cell msi cancer

• Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

  PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups

  Has reproduction

  A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.

  tcga-blca blca tcga deep transfer-learning neural-network