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).

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

  PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

  mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq

• Point mutations in GLI3 lead to misregulation of its subcellular localization.

  PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

  Full-text index only

  The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

  hela immunofluorescence real-time luciferase

• Antibody binding loop insertions as diversity elements.

  PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

  Full-text index only

  A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

  gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface

• Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

  PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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  Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

  chinese tissues skeletal pk15 full-length real-time gfp

• Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

  PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

  Has reproduction · 93

  An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

  hff mrc5 chip-qpcr rt-qpcr chipseq

• 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

  PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups

  Has reproduction · 78

  A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.

  interrogans canine syrian smrt bulk rt-qpcr

• RIT1 controls actin dynamics via complex formation with RAC1/CDC42 and PAK1.

  PMID 29734338 · PMC5937737 · PLoS genetics · 2018 · 8 claims · 8 setups

  Has reproduction

  PAK1 is a novel direct effector of RIT1

  hek293t cos7 his-tagged western gst co-immunoprecipitation

• Identification of new ETV6 modulators through a high-throughput functional screening.

  PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

  reh genome-wide qrt-pcr chip-seq

• Neuronal Small RNAs Control Behavior Transgenerationally.

  PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups

  Has reproduction · 49

  Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations

  elegans prab-3 dissected worms small sequencing facs

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

  Full-text index only

  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Functional analysis of the novel TBX5 c.1333delC mutation resulting in an extended TBX5 protein.

  PMID 18828908 · PMC2567295 · BMC medical genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  c.1333delC is a novel de novo frameshift mutation in TBX5 exon 9 predicted to produce an elongated 580-amino-acid protein (74 miscoding + 62 supernumerary C-terminal residues) instead of a truncated one

  peripheral cos-7 direct confocal co-localization

• Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

  PMID 18362173 · PMC2292215 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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  Somatic JAK1 mutations occur in ALL and are more prevalent among adult T-cell precursor ALL (T-ALL) than B-ALL

  genomic jak1-deficient u4c bw5147 dhplc stat1 cytokine-independent

• Functional restoration of BRCA2 protein by secondary BRCA2 mutations in BRCA2-mutated ovarian carcinoma.

  PMID 19654294 · PMC2754824 · Cancer research · 2009 · 8 claims · 7 setups

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  Secondary BRCA2 mutations restore BRCA2 protein/reading frame and thereby cause acquired platinum and PARP inhibitor resistance in BRCA2-mutated ovarian carcinoma

  ovarian peo1 v-c8-dr-gfp western brca2 crystal

• Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

  PMID 36373634 · PMC9723646 · Nucleic acids research · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells (OSCs)

  drosophila ovarian osc melanogaster chip-seq sirna western

• A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation.

  PMID 36149401 · PMC9576273 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  A C-terminal patch of the LRRK2 Armadillo domain (residues ~350–550, 'site #1') binds non-phosphorylated Rab29, Rab8A, and Rab10 with low-micromolar affinity

  recombinant lrrk2 hela hek293t microscale confocal immunoblotting

• Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

  PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

  Full-text index only

  XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

  hct116 macaque cos-7 genomic cdna est molecular

• Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

  PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

  Full-text index only

  OPTC is a candidate gene involved in POAG pathogenesis

  genomic pcr optc retinal pcr-sscp dhplc sequencing

• Mutations in UCP2 in congenital hyperinsulinism reveal a role for regulation of insulin secretion.

  PMID 19065272 · PMC2588657 · PloS one · 2008 · 6 claims · 5 setups

  Full-text index only

  Heterozygous UCP2 coding variants (parentally inherited) were identified in 2 of 10 CHI patients with no mutations in known CHI genes

  peripheral saccharomyces yeast ins-1e dhplc proton western

• Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins.

  PMID 32773039 · PMC7438113 · eLife · 2020 · 7 claims · 3 setups

  Has reproduction · 87

  Drosophila female germline stem cells lack canonical Polycomb silencing and have a non-canonical H3K27me3 distribution resembling early embryos.

  drosophila facs-purified hsgfp germline-specific chipseq