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).

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae.

  PMID 37240377 · PMC10218906 · International journal of molecular sciences · 2023 · 7 claims · 8 setups

  Full-text index only

  HyperTRIBE was successfully established in S. cerevisiae by fusing an RBP to the hyper-active catalytic domain of human ADAR2 (E488Q), marking target transcripts with A-to-G editing events detectable by high-throughput sequencing

  cerevisiae khd1 wild-type bfr1-heterozygous hypertribe western meme

• Exploring microproteins from various model organisms using the mip-mining database.

  PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups

  Has reproduction · 85

  Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions

  nine cerevisiae thaliana bulk transcriptome growth

• A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length.

  PMID 38638702 · PMC11025885 · NAR genomics and bioinformatics · 2024 · 8 claims · 7 setups

  Has reproduction · 98

  Ribosome drop-off events occur at a significant rate in S. cerevisiae cultured in standard conditions

  cerevisiae ribo-seq ribosome rna-seq read

• 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

  haploid pooled colony bulk pooled

• Foster thy young: enhanced prediction of orphan genes in assembled genomes.

  PMID 34928390 · PMC9023268 · Nucleic acids research · 2022 · 7 claims · 8 setups

  Has reproduction · 84

  Each of the five gene-prediction pipelines under-predicts orphan genes, with detection as low as 11% under one prediction scenario.

  arabidopsis saccharomyces oryza direct braker maker

• An extensive evaluation of read trimming effects on Illumina NGS data analysis.

  PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.

  homo arabidopsis prunus saccharomyces rna-seq snp novo

• Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.

  PMID 30576656 · PMC6310685 · Molecular cell · 2018 · 8 claims · 8 setups

  Has reproduction

  Depletion of Rap1 induces divergent noncoding transcription at a large fraction of Rap1-regulated gene promoters

  cerevisiae rap1-aid northern western poly

• GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.

  PMID 33758032 · PMC8547006 · mSystems · 2021 · 8 claims · 7 setups

  Has reproduction · 70

  GAUGE automatically annotates GEO microbial transcriptomic data sets (microarray and RNA-seq), increasing the proportion of annotatable studies from 4% to 33%

  microarray rna-seq aeruginosa mantel manual anova

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data.

  PMID 29420797 · PMC5961211 · Nucleic acids research · 2018 · 7 claims · 5 setups

  Has reproduction · 68

  Octopus-toolkit is a stand-alone application that automatically retrieves and processes large sets of epigenomic and transcriptomic NGS data from GEO in a single step

  mammary liver saccharomyces chip-seq rna-seq

• The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

  PMID 30899024 · PMC6428865 · Nature communications · 2019 · 7 claims · 8 setups

  Has reproduction · 85

  Xrn1 promotes translation of a specific group of mRNAs encoding membrane/secretome proteins, acting at translation initiation.

  cerevisiae yeast xrn1∆ western luciferase polysome