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).

• Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

  PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups

  Has reproduction · 75

  RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.

  pbmcs pbmc aligned bulk read transcript

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

  Full-text index only

  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

  PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 74

  RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

  pericarp green cuiguan illumina bulk qrt-pcr light

• Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.

  PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 52

  A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity

  vespid single-copy brain caste-biased bulk orthology principal

• Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

  PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

  Full-text index only

  Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

  peripheral blood pooled trio gene quantitative promoter

• High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

  PMID 17702760 · PMC2018616 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  An integrated strategy combining en masse pentapeptide insertion mutagenesis, yeast two-hybrid screening, and parallel genetic footprinting can map protein-protein interfaces at amino acid precision and is generally applicable to any interacting protein pair.

  saccharomyces plasmid pooled individual yeast pcr-based restriction

• Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

  PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups

  Has reproduction · 68

  Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.

  cerevisiae colony-forming-unit bulk pooled

• De novo identification of CD4(+) T cell epitopes.

  PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

  Has reproduction · 83

  SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

  nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species

• A DNA microarray survey of gene expression in normal human tissues.

  PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

  normal common computational each two-color comparative unsupervised

• Proteomic approaches to cancer biomarkers.

  PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups

  Full-text index only

  Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.

  plasma serum capan-2 apcδ580 lectin silac elisa

• High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.

  PMID 35776646 · PMC9243297 · STAR protocols · 2022 · 8 claims · 8 setups

  Has reproduction · 65

  HT-SELEX enables unbiased, in vitro determination of preferred DNA target motifs for DNA-binding proteins by iterative selection and PCR amplification of bound oligonucleotides

  synthetic pcr-generated selex histidine-tagged pcr polyacrylamide spectrophotometry

• Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

  PMID 35701420 · PMC9197839 · Scientific data · 2022 · 8 claims · 5 setups

  Has reproduction · 50

  An open, containerised, Nextflow-orchestrated reanalysis pipeline combining metadata annotation, SWATH-MS analysis, statistical analysis, and Expression Atlas integration was developed for public DIA data.

  pooled datasets pxd014194 technical swath-ms dda-based differential

• transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.

  PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups

  Has reproduction · 95

  transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms

  piper assembled longum predicted rna-seq novo transcriptome

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse