Summary:

A public repository of data processed for Mallm, Iskar, Ishaque et. al. 2018 Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks

Website: http://www.cancerepisys.org/cancerepisys/index.html

Github: https://github.com/CancerEpiSys/Mallm-et-al-processing-scripts

Research mission

CancerEpiSys is a BMBF funded research project with the CancerSys program that dissects the epigenetic networks associated with chronic lymphocytic leukemia (CLL) to develop novel diagnostic and therapeutic approaches for the disease. It has been initiated based on the emerging view that signals encoded in the DNA sequence, epigenetic modifications (e.g. DNA methylation, post-translational histone modifications), non-coding RNAs and nucleosome positioning are not independently regulated properties. Rather, these chromatin features are governed by an interconnected network of molecular processes that determine the cellular gene expression program. Any errors that occur in the interplay of these factors can lead to aberrant gene regulation associated with cancer. To rationalize the mode of action of novel ‘epigenetic’ drugs in cancer therapy that change properties of this network, we will dissect experimentally and mathematically the interdependence of these processes, focusing on CLL.

The main objectives of CancerEpiSys are: (i) deciphering the relation of DNA sequence, epigenetic modifications, nucleosome positioning and aberrant gene expression in CLL, (ii) the identification of epigenetic network morphologies that describe the response to the epigenetic drugs panobinostat and 3-deazaneplanocin (DZNep) that inhibit histone deacetylases and methyltransferases, (iii) the characterization of epigenetic markers and chromatin features of CLL patient subgroups, and (iv) the integration of results into an analysis scheme for the epigenetic aberrations most relevant for prognostication, prediction of treatment relapse and stratification of patients with respect to therapeutic options. Moreover, our results will inform novel therapeutic approaches that target gene-expression programs at the epigenetic level to sensitize cancer cells towards apoptosis and anti-growth signals.

Summary:

Magnetic resonance imaging scan of a baboon brain (Papio papio) from http://braincatalogue.org/Baboon

Summary: The effect of consumer diversity on the ecosystem functioning of salt marshes on Sapelo Island, Georgia. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/717035

Summary:

Weighted brain network matrices for all subjects reconstructed using each pipeline. Filename letters denote the combination of pipeline stages used to reconstruct the matrix, whereas the number represents the subject. Pipeline stages are described in filename_key.txt. The brain region names and parcellation labels corresponding to the network node row/column are in X_region_names.txt and X_parcellation_labels.txt, where X is the atlas abbreviation described in filename_key.txt.
 

Summary:

This is an interactive excel file that can be used to estimate the costs of various scenarios of expanded testing for COVID-19. Several sensitivity analyses are possible. Testing is enabled for populations of various size and COVID-19 prevalence. In this version, data is current for Canada and all provinces to May 8, 2020.

Summary:

This is an interactive excel file that can be used to estimate the costs of various scenarios of expanded testing for COVID-19. Several sensitivity analyses are possible. Testing is enabled for populations of various size and COVID-19 prevalence. In this version, data is current for Canada and all provinces to July 17, 2020.

Summary:

Magnetic Resonance Imaging Scan of a Blackbuck (Antilope cervicapra) from http://braincatalogue.org/Blackbuck

Summary:

Archive of integrated manuscript, code, and data as an R package. This release corresponds with the revised journal submission version.

Summary: These data include measurements of juvenile oyster shell strength from a dose response experiment of varying blue crab urine concentrations conducted at Dauphin Island Sea Lab, Dauphin Island, AL in August - Oct 2022. Study description: Metabolites from blue crab urine are known to cause shell strengthening in juvenile oysters as a defensive response. Previous studies have identified several bioactive molecules in urine that induce this response in oysters, but others have yet to be identified. In the current study, an array of concentrations of blue crab urine was used to treat oyster juveniles in order to assess the dose-dependency of this response. Oysters were exposed to urine treatments for 8 weeks and their shell strength (N) was measured and standardized to the size of the animals (mm) as a proxy for understanding this defense. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/884015

Summary: Fig 1. Myanmar study sites. Map of bat capture sites in Myanmar, 2016–2018. Data Sources: Natural Earth. Map created in QGIS 2.18.4. 2020. https://doi.org/10.1371/journal.pone.0230802.g001

Summary: Mesophotic coral reefs, defined as deep reefs between 30 and 150 m, are found worldwide and are largely structured by changes in the underwater light field. Additionally, it is increasingly understood that reef-to-reef variability in topography, combined with quantitative and qualitative changes in the underwater light field with increasing depth, significantly influence the observed changes in coral distribution and abundance. Here we take a modeling approach to examine the effects of the inherent optical properties of the water column on the irradiance that corals are exposed to along a shallow to mesophotic depth gradient. In particular, the roles of reef topography including horizontal, sloping and vertical substrates are quantified as well as the differences between mounding, plating and branching colony morphologies. Downwelling irradiance and reef topography interact such that for a water mass of similar optical properties the irradiance reaching the benthos varies significantly with topography (i.e., substrate angle). Corals with different morphologies also interact with these benthic irradiances; model results show that isolated hemispherical colonies consistently “see” greater irradiances across depths, and throughout the day, compared to plating and branching morphologies. The differences in the photoautotrophic potential of different coral morphologies, based on the changes in irradiance modelled here, are not, however, consistent with depth-dependent distributions of these coral morphotypes. Other factors (e.g., heterotrophy) arguably contribute, but irradiance driven patterns are a strong proximate cause for the observed differences in mesophotic communities on sloping versus vertical reef substrates. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/841083

Summary: Cyprinodon variegatus offspring growth rate from parental contribution experiments conducted on wild caught Atlantic specimens during 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/709815

Summary: Offspring growth rate from experiments testing for local adaptation in thermal TGP For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/704653

Summary: Proximate biochemistry of sponge species collected in 2017 and 2018 across the Caribbean Basin in Curacao, Belize, Grand Cayman, St. Croix. These data were published in Clayshulte Abraham et al. (2021). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/868047

Summary: Cyprinodon variegatus offspring growth rate from coloration discovery experiments conducted on specimens wild caught from the Atlantic in 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/709737

Summary: Cyprinodon variegatus offspring growth rate in grandparantal experiments from specimens wild caught in the Atlantic during 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/709762

Summary: These data include measurements of juvenile oyster shell strength from a dose response experiment conducted at Dauphin Island Sea Lab, Dauphin Island, AL in June - August of 2021. Study description: Homarine and trigonelline are two blue crab urine metabolites that cause juvenile oysters to strengthen their shells are a defensive response. We evaluated the dose dependency of this response with a dose-response experiment where homarine and trigonelline concentrations (of each individual chemical and a combination of the two) spanned 5 log half-steps. Juvenile oysters were exposed to chemicals for 8 weeks and their shell strength (N) was measured and standardized to the size of the animals (mm) as a proxy for understanding this defense. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/883999

Summary: These data include measurements of juvenile oyster shell strength from predator cue bioassay experiments conducted at Dauphin Island Sea Lab, Dauphin Island, AL between June and August of 2020. Study description: Homarine and trigonelline are two blue crab urine metabolites that cause mud crabs to seek refuge, but it is unknown whether these molecules influence other species. In the current study, homarine, trigonelline, and blue crab urine of animals fed conspecific and heterospecific diets were tested on juvenile oysters to ascertain if the same molecules known to alter mud crab behavior also affect oyster morphology. Juvenile oysters were exposed to chemicals for roughly 6 weeks and their shell strength (N) was measured and standardized to the size of the animals (mm) as a proxy for understanding this defense. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/883945

Summary: Compensatory growth and TGP data from experiments conducted on juvenile Cyprinodon variegatus that were wild caught in the Atlantic during 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/709707

Summary: Cyprinodon variegatus offspring growth rate from 5 generation increasing temperature experiments conducted on Atlantic wild caught specimens during 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/709787