iScience

Unmodified data relating to the iScience manuscript titled "Mapping the substrate landscape of protein phosphatase 2A catalytic subunit PPP2CA"

[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

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.

IsSupplementTo: Diomedi, S., Vaccari, F. E., Filippini, M., Fattori, P., Galletti, C. (2020). Mixed Selectivity in Macaque Medial Parietal Cortex during Eye-Hand Reaching. IScience, 23(10), 101616. (https://doi.org/10.1016/j.isci.2020.101616)

Human activities increasingly challenge wild animal populations by disrupting ecological connectivity and population persistence. Yet, human-modified habitats can provide resources, resulting in selection of disturbed areas by generalist species. To investigate spatial and temporal responses of a generalist carnivore to human disturbance, we investigated habitat selection and diel activity patterns in caracals (Caracal caracal). We GPS-collared 25 adults and subadults in urban and wildland-dominated subregions in Cape Town, South Africa. Selection responses for landscape variables were dependent on subregion, animal age class, and diel period. Contrary to expectations, caracals did not become more nocturnal in urban areas. Caracals increased their selection for proximity to urban areas as the proportion of urban area increased. Differences in habitat selection between urban and wildland caracals suggest that individuals of this generalist species exhibit high behavioral flexibility in response to anthropogenic disturbances that emerge as a function of habitat context.

This repository contains data described in this study: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia. Ennis S et. al., iScience, 2023. DOI: 10.1016/j.isci.2023.106943. Contents: bone_marrow.h5ad - AnnData file with the integrated dataset ref_model_final.tar.gz - A zipped folder containing the scVI model for the integrated dataset Supplemental_material.tar.gz - A zipped folder containing the supplemental figures and tables from the publication

IsSupplementTo: Diomedi, S., Vaccari, F. E., Filippini, M., Fattori, P., Galletti, C. (2020). Mixed Selectivity in Macaque Medial Parietal Cortex during Eye-Hand Reaching. IScience, 23(10), 101616. (https://doi.org/10.1016/j.isci.2020.101616)

Three-dimensional reconstruction models of cyanobacteria from a 407 million year old fossil from the Lower Devonian Rhynie chert, UK. Thin sections SU.PB. 2023.0.1.2.8 from the Palaeobotany Collection in the Pôle Collections scientifiques et patrimoniales. Bibliothèque de Sorbonne Université, Paris (France). Imaris files (.IMS) can be viewed using the Imaris Viewer software, freely available in both Windows and Mac versions from https://imaris.oxinst.com/imaris-viewer.

This repository contains data described in this study: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia. Ennis S et. al., iScience, 2023. DOI: 10.1016/j.isci.2023.106943. Contents: bone_marrow.h5ad - AnnData file with the integrated dataset ref_model_final.tar.gz - A zipped folder containing the scVI model for the integrated dataset