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).

• Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

  PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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  Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

  genome poly est cdna est blast cdna

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

  PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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  Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

  ductal same sporadic paired cdna quantitative genotyping

• cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer.

  PMID 19671129 · PMC2731783 · BMC cancer · 2009 · 8 claims · 6 setups

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  cDNA sequencing detects P53 missense mutations in colorectal cancer more frequently and reliably than DNA sequencing

  colorectal paired sequencing cdna real-time

• Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

  PMID 38940130 · PMC11256924 · Bioinformatics (Oxford, England) · 2024 · 7 claims · 5 setups

  Has reproduction · 87

  Forseti is the first probabilistic model for resolving the splicing status of exonic scRNA-seq reads by scoring putative fragments linking read alignments to proximate priming sites

  training simulated held-out paired-end cubic mlp

• p53 tumor suppressor gene mutations in fibroblast-like synoviocytes from erosion synovium and non-erosion synovium in rheumatoid arthritis.

  PMID 15642132 · PMC1064878 · Arthritis research & therapy · 2005 · 8 claims · 4 setups

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  p53 mutation frequency and type do not differ significantly between erosion and non-erosion FLS

  fibroblast-like matched snap-frozen p53 elisa pcr

• 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

• High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer.

  PMID 11207044 · PMC2363776 · British journal of cancer · 2001 · 8 claims · 4 setups

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  The SAFB locus region on chromosome 19p13.2-3 shows a very high rate of loss of heterozygosity (LOH) in primary breast cancer, indicating presence of a breast tumour-suppressor gene locus

  breast microdissected loh rt-pcr pcr

• Finding disease candidate genes by liquid association.

  PMID 17915034 · PMC2246280 · Genome biology · 2007 · 7 claims · 6 setups

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  LA can detect functionally associated genes that are not directly co-expressed by identifying a mediating gene Z whose expression level changes the correlation between X and Y.

  nci_cdna gnf_2002 finnish gnf_2004 liquid transmission correlation

• RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

  PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 41

  Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

  pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry

• Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

  PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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  B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

  paraffin-embedded cloned same predicted pcr cloning blastx

• Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

  PMID 7669582 · PMC2033876 · British journal of cancer · 1995 · 8 claims · 5 setups

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  A novel missense mutation (TGG→CGG, Trp133→Arg) in nm23-H2 was found in one stage III serous ovarian carcinoma

  ovarian case matched same pcr-sscp subcloning loh

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

  PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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  PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

  pax6 brain yeast sequence yeast semi-quantitative

• Targeted disruption of the S1P2 sphingosine 1-phosphate receptor gene leads to diffuse large B-cell lymphoma formation.

  PMID 19903857 · PMC2973841 · Cancer research · 2009 · 8 claims · 8 setups

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  S1P2−/− mice develop clonal B-cell lymphomas with age, with ~half affected by 1.5-2 years

  s1p2− lymphoma bone genomic necropsy histology flow