Single Cell RNAseq BAM files and processed data file for "Low intracellular calcium is an essential feature of hematopoietic stem cells"
Contributors: Hans Snoeck
... The two .bam files uploaded contain aligned sequence data for sc-RNAseq of phenotypic HSCs sorted from culture after 14 days in high and low calcium chloride media. The excel file contains the differential expression analysis of genes extracted from the three gene clusters (Cluster A, B, C) identified by multidimensional data visualization and analysis.
Contributors: Frederik Leliaert
... Alignments, trees and Biogeobears analyses related to the study "Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria". Biogeographical processes underlying Indo-Pacific biodiversity patterns have been relatively well studied in marine shallow water invertebrates and fishes, but have been explored much less extensively in seaweeds, despite these organisms often displaying markedly different patterns. Using the marine red alga Portieria as a model, we aim to gain understanding of the evolutionary processes generating seaweed biogeographical patterns. Our results will be evaluated and compared with known patterns and processes in animals. Species diversity estimates were inferred using DNA-based species delimitation methods. Historical biogeographical patterns were inferred based on a six-gene time-calibrated phylogeny, distribution data of 802 specimens, and probabilistic modelling of geographic range evolution. The importance of geographic isolation for speciation was further evaluated by population genetic analyses at the intraspecific level. We delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo-Malay Archipelago (IMA). Our phylogeny indicates that Portieria originated during the late Cretaceous in the area that is now the Central Indo-Pacific. The biogeographical history of Portieria includes repeated dispersal events to peripheral regions, followed by long-term persistence and diversification of lineages within those regions, and limited dispersal back to the IMA. Our results suggest that the long geological history of the IMA played an important role in shaping Portieria diversity. High species richness in the IMA resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both ‘centres of origin’ and ‘centres of accumulation’, and corroborate previous findings for invertebrates and fish that there is no single unifying model explaining the biological diversity within the IMA.
Contributors: Benjamin Marshall, Nicholas Casewell, Miguel Vences, Frank Glaw, Franco Andreone, Andolalao Rakotoarison, Giulia Zancolli, Friederike Woog, Wolfgang Wüster
... This dataset include the raw sequences that cover the H1-H2 of Na+/K+-ATPase for Malagasy Species. For birds, mammals and amphibians the alpha 1 isoform was sequenced. The squamate sequences correspond to the alpha 3 isoform.
Contributors: Denise Kühnert, Tanja Stadler, John Metcalfe, Lukas Fenner, Sebastien Gagneux, Daniela Brites, David Stucki, Mireia Coscolla
... SNP alignments of M. tuberculosis outbreak data sets.
Contributors: Muhammad Arslan
... Transcriptome of Juncus effusus. Plant tissues (roots and shoots) were harvested from individuals at the vegetative developmental stage representing in total 18 genotypes that were raised from seeds collected in the field.
Contributors: Lu Zeng, Dan Kortschak, Joy Raison, Terry Bertozzi, David Adelson
... 1) Files begin with 'all_retrovirus.' in 'report_run' are data we used to identify retrovirus (see detail in supplementary 1.5.3); 2) Files begin with 'GB_TE.new' in 'GBTE_data' are index files we used to identify reverse transcriptase and TE sequences from NCBI (see detail in supplementary 1.5.3); 3) 'report_run' are codes used to run reportsJ.pl (see detail in supplementary 1.5.3); 4) Files begin with 'sprot.' in 'report_run' are index files we used to identify proteins (see detail in supplementary 1.5.3); 5) 'Vertebrate_use.fa' is Vertebrate repeat consensus sequences downloaded from Repbase, we used it as CENSOR library (see detail in supplementary 1.5.1); 6) 'our_known_reps_20130520' was used in the first CENSOR run (see detail in supplementary 1.5.1). 7) 'RepBase20.04.fasta' used in last step of TE annotation, contains CENSOR TE references
The CST complex mediates end-protection at double-strand breaks and promotes PARP inhibitor sensitivity in BRCA1-deficient cells. DOI: https://doi.org/10.1016/j.celrep.2018.04.046
Contributors: Sven Rottenberg, Marco Barazas
... Original data used for plotting the figures belonging to the study "The CST complex mediates end-protection at double-strand breaks and promotes PARP inhibitor sensitivity in BRCA1-deficient cells".
GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans
Contributors: Miguel Vasconcelos Almeida
... Original data included in Almeida et al. 2018.
Data for: De novo design of selective Sortase-A Inhibitors: Synthesis, structural and in vitro characterization
Contributors: Kranthi Raj Kodamala, Pardhasaradhi Mathi, Dr Ramachandran Dittakavi, Ravi M, Mahendran Botlagunta, Veera Venkata Vara Prasad Mutyala
... Highest active compound was docked into the protein structure.
Contributors: Ki-Oug Yoo, Andrew Crowl, Kyung-Ah Kim, Kyeong-Sik Cheon, Nico Cellinese
... Phylogenetic and biogeographic analyses were conducted to provide insights into the evolution and historical biogeography of East Asian taxa in the Campanuloideae (Campanulaceae). A molecular dataset including nuclear PPR70 gene sequences and five plastid regions (atpB, matK, petD, rbcL, and trnL-trnF) was assembled. Data: 1 - Area matrix for biogeographic analysis in BioGeoBears; 2 - Plastid alignment for phylogenetic analysis; 3 - Nuclear (PPR70) alignment for phylogenetic analysis; 4 - Plastid plus nuclear (PPR70) combined alignment for phylognetetic analysis;