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iScience

ISSN: 2589-0042

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Datasets associated with articles published in iScience

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1970
2025
1970 2025
3 results
  • Mapping the substrate landscape of protein phosphatase 2A catalytic subunit PPP2CA
    Unmodified data relating to the iScience manuscript titled "Mapping the substrate landscape of protein phosphatase 2A catalytic subunit PPP2CA"
  • Decoding the Inversion Symmetry Underlying Transcription Factor DNA-Binding Specificity and Functionality in the Genome
    [Column E and Column F] We overlapped the location coordinates of the 81,922 0-nt to 5-nt variant 13-nt ERE or HRE DNA elements in the genome and the location coordinates of the ChIPSeq or ChIPExo peaks in an experiment (157 ER experiments at 0-nt to 5-nt variant ERE DNA elements) (194 KR experiments at 0-nt to 5-nt variant HRE DNA elements) to determine the absolute number of times each 0-nt to 5-nt variant 13-nt ERE or HRE DNA element occurred within an experiment (the entire 13-nt DNA element was required to be within the peak boundaries). [Column V] Multiple peak selection criteria were used (L4, L8, L10, L15, L20), where Lx represents an x-fold greater tag density at peaks than in the surrounding 10-kb region. This performs a low-to-high stringency analysis of the data. By studying the data with respect to a multiple spectrum of peak selection criteria, we adjust for both the risk of excess background noise and the risk of filtering out any low-amplitude information. All peaks are observed at L4, [Column V] identifies whether that specific peak is also observed at L8, L10, L15 or L20. The ChIPSeq or ChIPExo peaks were annotated to regions in the genome (annotatePeaks.pl) using Homer. [Column A] Peak ID [Column B] Chromosome [Column C] Peak start position [Column D] Peak end position [Column G] Strand [Column H] Peak Score [Column I] FDR/Peak Focus Ratio/Region Size [Column J] Annotation (i.e. Exon, Intron, ...) [Column K] Detailed Annotation (Exon, Intron etc. + CpG Islands, repeats, etc.) [Column L] Distance to nearest RefSeq TSS [Column M] Nearest TSS: Native ID of annotation file [Column N] Nearest TSS: Entrez Gene ID [Column O] Nearest TSS: Unigene ID [Column P] Nearest TSS: RefSeq ID [Column Q] Nearest TSS: Ensembl ID [Column R] Nearest TSS: Gene Symbol [Column S] Nearest TSS: Gene Aliases [Column T] Nearest TSS: Gene description [Column U] Nearest TSS: Gene type
  • Data from Babin, Piganeau et al. "Chromosomal translocation formation is sufficient to produce fusion circular RNAs specific to patient tumor cells"
    These data are linked to our paper "Chromosomal translocation formation is sufficient to produce fusion circular RNAs specific to patient tumor cells" from Babin et al; iScience 2018 Each figure raw data sets are available.