Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1246973 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Phylogenetic relationships of the Mexican tussilaginioids (Asteraceae)
| PRJEB25760 | ENA
Project description:The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia - a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together these should broadly enable large-scale mammalian lineage tracing efforts.Cassiopeia and its benchmarking resources are publicly available at https://www.github.com/YosefLab/Cassiopeia.
2020-03-11 | GSE146712 | GEO
Project description:Genome profiling of primary tumors and matched metastases from a BALB-NeuT murine breast cancer transplantation model. The first goal of this study was to investigate the differences of primary tumors and metastases with regard to copy number alterations. The second goal was to infer phylogenetic trees reflecting the evolutionary paths of primary tumors and their derived metastases (only mice with at least one metastasis were used for phylogenetic analyses).
2016-09-30 | GSE87469 | GEO
Project description:There are very few studies exploring the genetic diversity of tick-borne encephalitis complex viruses. Most of the viruses have been sequenced using capillary electrophoresis, however, very few viruses have been analyzed using deep sequencing to look at the genotypes in each virus population. In this study, different viruses and strains belonging to the tick-borne encephalitis complex were sequenced and genetic diversity was analyzed. Shannon entropy and single nucleotide variants were used to compare the viruses. Then genetic diversity was compared to the phylogenetic relationship of the viruses.
2023-12-04 | E-MTAB-12112 | biostudies-arrayexpress
Project description:Purpose: To investigate the quaternary structures of Rhodopsin-family GPCRs. Method: Analyzed 60 receptors from HEK 293T cells. Results: 1) Most of these receptors are monomers. 2) The phylogenetic distribution of dimers suggests that monomers have an evolutionary advantage due to constraints imposed by dimerization on rates of receptor diversification.
2017-08-10 | GSE102461 | GEO
Project description:Mycelia of filamentous fungi explore new substrates by means of hyphae that extend from the periphery of the colony. Previously, it has been shown by immuno-labelling, reporter studies and in situ hybridization that these exploring hyphae are heterogenic with respect to protein secretion and transcription. We performed single hyphal tip RNA profiling using microarrays to assess the differences in RNA accumulation in neighboring exploring hyphae Single tips from 5 neighboring exploring hyphae from a single colony were selected for RNA extraction, amplification and hybridization on Affymetrix microarrays
2011-05-17 | E-GEOD-25497 | biostudies-arrayexpress