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).

• Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

  PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

  Has reproduction · 70

  AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

  head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr

• Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

  PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

  Full-text index only

  Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

  peripheral genomic ebv-transformed conformation pira-pcr rt-pcr

• Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.

  PMID 33779545 · PMC8049744 · eLife · 2021 · 8 claims · 6 setups

  Has reproduction · 100

  The initial transcriptional and chromatin response to mid-gastric bisection is identical at oral and aboral wounds at 3 hpa and only diverges by 8 hpa.

  hydra rna-seq atac-seq transcription

• Independent component analysis reveals new and biologically significant structures in micro array data.

  PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

  Full-text index only

  ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

  acute serum-stimulated head aml microarray clust term

• Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

  PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 87

  Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

  breast lung colorectal melanoma single-cell gene reactome

• Integrated omics in Drosophila uncover a circadian kinome.

  PMID 32483184 · PMC7264355 · Nature communications · 2020 · 8 claims · 6 setups

  Has reproduction · 98

  iCMod, a computational pipeline integrating transcriptomic, proteomic, and phosphoproteomic circadian data, was developed to accurately identify normalized circadian p-sites (NCPs)

  drosophila analysis tmt-based sequencing western

• High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

  PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups

  Has reproduction · 87

  mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.

  c57bl strand-specific pol computational

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes by a discriminative index (DI) score representing classification power for distinguishing given groups, enabling intuitive selection of optimal biomarker genes.

  tcga melanoma lung head bulk single-cell rna-seq

• Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

  PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.

  sheep genome bac sequence randomization

• Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

  PMID 16288662 · PMC1322226 · BMC evolutionary biology · 2005 · 7 claims · 5 setups

  Full-text index only

  Proteins with extended coiled-coil domains (>250 amino acids) are largely absent from bacterial genomes but present in archaea and eukaryotes.

  proteomes predicted long prokaryotic coiled-coil all-against-all sequence