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).

• Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer

• CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

  PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 62

  CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons

  cask ko1 day mature bulk qrt-pcr western

• Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

  PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 83

  188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways

  blood degs peripheral hub microarray kegg cibersort

• Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome.

  PMID 36611783 · PMC9817706 · Animals : an open access journal from MDPI · 2023 · 8 claims · 6 setups

  Has reproduction · 71

  1442 genes were differentially expressed in AS broiler lung vs normal lung (614 up-regulated, 828 down-regulated)

  lung left blood heart sequencing functional quantitative

• Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.

  PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance

  merged gse45827 superior differential feature comparative

• Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

  PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

  Full-text index only

  Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

  squamous ophid degs oligonucleotide interaction connectivity

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.

  PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups

  Has reproduction · 46

  De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases

  sparassis latifolia bulk transcriptome sequence

• A2TEA: Identifying trait-specific evolutionary adaptations.

  PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups

  Has reproduction · 90

  A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment

  user-provided multi-species genes sequences rna-seq orthologous phylogenetic

• Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.

  PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups

  Has reproduction · 78

  Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings

  chinensis physiological relative bulk