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).

• Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

  PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

  Has reproduction · 50

  2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

  flower roots analysis parental high-throughput quantitative pcr

• Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

  PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

  Full-text index only

  Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

  genomic phylogenetic direct high

• Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.

  PMID 17010193 · PMC1599749 · BMC cancer · 2006 · 8 claims · 4 setups

  Full-text index only

  No germline deleterious mutations were identified in the ATR coding region among 54 non-BRCA1/2 high-risk French Canadian breast cancer cases.

  genomic ebv-transformed normal direct linkage rt-pcr

• Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer.

  PMID 18489799 · PMC2413254 · BMC cancer · 2008 · 8 claims · 6 setups

  Full-text index only

  Pathogenic BRCA1/BRCA2 mutations were identified in 294 of 1,010 (29.1%) unrelated high-risk Czech probands

  genomic pcr-amplified brca1 pha-stimulated truncation heteroduplex direct

• Sequence variations of GRM6 in patients with high myopia.

  PMID 19862333 · PMC2765235 · Molecular vision · 2009 · 7 claims · 8 setups

  Full-text index only

  Three novel GRM6 variations with predicted functional consequences (c.67-82delCAGGCGGGCCTGGCGCinsT, c.858-5a>g, c.1537G>A) were found in high myopia patients but absent in 96 controls

  genomic pcr mglur6 grm6 pcr heteroduplex pcr-restriction

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• Neuroscience in the era of functional genomics and systems biology.

  PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

  Full-text index only

  Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

  developing hippocampus bac-transgenic fetal situ gene bac-transgenic

• BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.

  PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts

  barley pacbio illumina read

• The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

  PMID 12381271 · PMC134458 · BMC genetics · 2002 · 7 claims · 8 setups

  Full-text index only

  UNC93A maps within the minimal region of allele loss on 6q27 between D6S264 and D6S149, centromeric to D6S149

  panel 293-t malignant same rt-pcr northern fluorescence

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species

• Advances in the study of SR protein family.

  PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

  Full-text index only

  SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

  nuclear bovine drosophila caenorhabditis selex rna-binding splicing

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Pegasys: software for executing and integrating analyses of biological sequences.

  PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

  Full-text index only

  Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

  eukaryotic formatted genomic input initio sequence gene

• Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

  PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

  Full-text index only

  Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

  qbl pgf classical ceph bac comparative gene

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.

  PMID 39057099 · PMC11276454 · Current issues in molecular biology · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  PTBP1 is significantly upregulated across multiple cancer types including LUAD, and higher PTBP1 levels are associated with worse LUAD patient survival

  cancer luad fibroblast a549 pan-cancer differential replicative

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp