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  • Matlab scripts used to analyze data associated with the manuscript entitled "A single cell atlas of the human liver tumor microenvironment". *please used Matlab 2019b to run the following m files. Files: inputData.mat: mat contains all raw and preprocessed data used in the study Create_Interactions_Network.m: Matlab script used to calculate Ligand-Receptor interaction score between different cell types. The script creates panels of Figure 3 and Table S5. Hepatocytes_Reconstruction.m: Matlab script used to reconstruct human hepatocytes zonation along the lobule axis. The script creates panel 'c' of Figure 4, Figure S4, and Table S7. Cancer_Cells_Spatial_Analysis.m: Matlab script used to calculate differential gene expression between malignant cells found at different zones (malignant border, malignant core, and fibrotic zone) captured by laser microdissection. The script creates panel 'd' of Figure 4 helperFunctions.zip: This folder contains required functions used by the m files.
    Data Types:
    • Software/Code
  • GTH-dependent follicle development begins with small antrum follicles and ends with preovulatory follicles. GTH-dependent follicle development is mainly controlled by gonadotropins, and the development time is 48h. The purpose of this study is to monitor the changes in gene expression of granulosa cells at four different time points during the GTH-dependent phase to increase our understanding of human GTH-dependent follicle development.Granulosa cell mRNA profiles of GTH-depend phase in mice.There are 12 samples represented four time points 0h (n=3), 12h (n=3), 24h (n=3) and 48h (n=3)
    Data Types:
    • Dataset
  • GTH-dependent follicle development begins with small antrum follicles and ends with preovulatory follicles. GTH-dependent follicle development is mainly controlled by gonadotropins, and the development time is 48h. The purpose of this study is to monitor the changes in gene expression of granulosa cells at four different time points during the GTH-dependent phase to increase our understanding of human GTH-dependent follicle development.Granulosa cell mRNA profiles of GTH-depend phase in mice.There are 12 samples represented four time points 0h (n=3), 12h (n=3), 24h (n=3) and 48h (n=3)
    Data Types:
    • Dataset
  • Young grapevines (Vitis vinifera) frequently die due to the crown gall (CG) disease induced by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbour a tumor-inducing (Ti) plasmid and cause formation of CGs due to genes encoded on the T-DNA. Expression of the oncogenes by transformed host cells induce cell proliferation, metabolic and physiological changes. The CG produces opines uncommon to plants, which provide an important nutrient source for A. vitis harbouring opine catabolism enzymes. CGs host a defined bacterial community and the mechanisms establishing a CG-specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the Ti-plasmid coexist in the genomes of the microbial species coexisting in CGs. We isolated eight bacterial strains from grapevine CGs, sequenced their genomes and tested their virulence and opine utilization ability in bioassays. In addition, the eight genome sequences were aligned to the sequences of a Ti-plasmid and seven published bacterial genomes, including closely related plant associated bacteria but not from CGs. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. By contrast, homologs of the opine catabolism genes were present in all strains including the non-virulent members of the Rhizobiaceae and non-Rhizobiaceae, indicating horizontal gene transfer of the opine degradation cluster from virulent to non-virulent strains. These results along with those of the opine utilization assay support the important role of opine utilization for co-colonization of virulent and non-virulent bacteria in CGs, thereby shaping the CG community. This dataset contains the prokka annotations of the genomes as used in "Opportunistic bacteria of grapevine crown galls are equipped with the genomic repertoire for opine utilization"
    Data Types:
    • Dataset
  • Data objects for the AHR project carried out by the group of Dr. Christiane Opitz (German Cancer Research Center) and collaborators.
    Data Types:
    • Dataset
  • The raw data of the datasets used for validating the AHR signature
    Data Types:
    • Dataset
  • The intermediate processed files for the manuscript: Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissues-of-origin
    Data Types:
    • Other
    • Dataset
  • eARGs2
    Data Types:
    • Other
    • Dataset
  • UMI-4C datasets generated in Sungalee et al. are provided as raw fastq sequencing files The following target_regions/lymphoma cell lines/conditions are available: BCL11A WSU-DLCL2 DMSO BCL11A WSU-DLCL2 A-485 48h BCL11A DoHH2 Vector BCL11A DoHH2 dCas9-KRAB sgRNA2 BCL11A K562 Vector BCL11A K562 dCas9-EP300 sgRNA2 BCL6/MYC FWD WSU-DLCL2 DMSO BCL6/MYC REV WSU-DLCL2 A485
    Data Types:
    • Dataset
  • RNASeq data from Sungalee et al. for lymphoma cell lines
    Data Types:
    • Dataset