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).

• In vivo application of RNA interference: from functional genomics to therapeutics.

  PMID 16096010 · PMC7112075 · Advances in genetics · 2005 · 7 claims · 7 setups

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  RNAi operates through two mechanistically related but distinct pathways: cytoplasmic delivery of siRNA duplexes and nuclear delivery of shRNA expression cassettes that mimic miRNA

  mice tumor laser-induced herpetic cationic intraperitoneal aqueous

• Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

  PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls

  activated skeletal muscle altered affymetrix quantitative sirna

• Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

  PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups

  Has reproduction · 85

  Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.

  liver huh-7 bulk sirna lipid

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• RNA interference in functional genomics and medicine.

  PMID 12808314 · PMC3055057 · Journal of Korean medical science · 2003 · 8 claims · 7 setups

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  RNAi is sequence-specific gene silencing induced by double-stranded RNA and is mediated by ~22-nt siRNAs generated from long dsRNA by the RNase III enzyme Dicer.

  caenorhabditis drosophila mammalian postnatal dsrna biochemical synthetic

• Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.

  PMID 36107487 · PMC9534548 · eLife · 2022 · 8 claims · 8 setups

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  Colorectal cancer (CRC) cells are coupled by gap junctions assembled predominantly from Cx26 (GJB2)

  colorectal normal crc microarray tcga single-cell

• Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

  PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

  cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

• Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

  PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

  hela protein-free dual-luciferase reporter thermodynamic

• A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

  PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

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  A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

  hela candidate screen genome-wide propidium sirna

• Crunching the bio-numbers.

  PMID 14664241 · PMC1316909 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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  The eTag Assay System rapidly identifies genes and related proteins without complex sample preparation or follow-up bioinformatics, unlike microarrays

  blood model brain lung etag sirna addl

• Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.

  PMID 32959884 · PMC7689298 · Human molecular genetics · 2020 · 8 claims · 8 setups

  Has reproduction · 67

  Trem2 R47H knock-in mice show gene dose-dependent decreased Trem2 expression in hippocampus, largely due to altered splicing

  hippocampal microglia conditioned rt-qpcr immunohistochemistry glial

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

  PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

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  The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

  hela sirna secondary synthetic

• Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

  PMID 19057677 · PMC2585813 · PLoS genetics · 2008 · 7 claims · 8 setups

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  Genome-wide siRNA screening identified 92 novel genes that support melanin production in human melanocytes with a low false discovery rate.

  mnt-1 melanocyte melanocytes genome-wide secondary quantitative

• Effect of PAIP1 on the metastatic potential and prognostic significance in oral squamous cell carcinoma.

  PMID 35153296 · PMC8841500 · International journal of oral science · 2022 · 8 claims · 8 setups

  Has reproduction · 10

  PAIP1 mRNA and protein levels are increased in OSCC/HNSCC tissues and cell lines compared to normal tissue/cells

  hnscc tcga cptac oscc microarray rna-seq quantitative

• Gene Regulatory Interactions at Lamina-Associated Domains.

  PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

  Has reproduction · 31

  Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

  adipose ascs mesenchymal chip-seq rna-seq atac-seq

• Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

  PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

  hela hs578t nih3t3 genomic chap-chip conventional scanning

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna