Surface metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA444390 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6958064_1.fastq.gz | Fastqsanger.gz | |||
| SRR6958064_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Solar panel surface microbial communities from Lawrence Berkeley National Laboratory, California, USA - R
| PRJNA444389 | ENA
Project description:Solar panel surface microbial communities from Lawrence Berkeley National Laboratory, California, USA - M
| PRJNA444388 | ENA
Project description:A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR. However, an unbiased diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for unbiased random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array developed at the Lawrence Livermore National Laboratory, California, USA, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for unbiased diagnostic analysis of all viruses in clinical samples.
2011-04-14 | GSE28597 | GEO
Project description:Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages: proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts. Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells.
2013-12-25 | GSE53635 | GEO
Project description:Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages: proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts. Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells. Erythroid differentiation stage-specific transcriptome analysis was performed by RNA-seq analysis of highly purified erythroblast populations
2013-12-25 | E-GEOD-53635 | biostudies-arrayexpress
Project description:1Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. 2Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. 3Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. 4CCTS Bioinformatic Program, The Rockefeller University, New York, NY 10065, USA. 5State Key Laboratory of Genetic Engineering & Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
2021-06-30 | GSE84157 | GEO
Project description:A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR. However, an unbiased diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for unbiased random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array developed at the Lawrence Livermore National Laboratory, California, USA, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for unbiased diagnostic analysis of all viruses in clinical samples. 19 clinical samples were analyzed for presence of virus using the MDA microarray. One of the samples is a negative control (water). One HCV-positive serum sample is included twice (HCV+1 and HCV+2).
2011-04-14 | E-GEOD-28597 | biostudies-arrayexpress
Project description:Root tissues, shoot tissues and root exudates were collected from hydroponically grown B. distachyon, M. truncatula and A. thaliana. Metabolites were extracted and analyzed by LCMS. Metabolites were separated on an Agilent 1290 stack using an Agilent InfinityLab Poroshell 120 HILIC-Z column (2.1 x 150 mm, 2.7 um). Detection was performed using a Thermo QExactive hybrid quadrupole-orbitrap mass spectrometer.
This data is has been incorporated into a manuscript (in preparation as of Dec 14, 2022):
The core metabolome and root exudation dynamics of
three phylogenetically distinct plant species
Sarah McLaughlin 1,2,3 , Kateryna Zhalnina 1,2 , Suzanne Kosina 1 , Trent R. Northen 1,2 *,
Joelle Sasse 1,2, 3 *
*corresponding authors: trnorthen@lbl.gov, jsasse@botinst.uzh.ch
1 Lawrence Berkeley National Laboratory, Environmental Genomics and Systems
Biology, 1 Cyclotron Road, Berkeley, CA, 94720, USA
2 Joint Genome Institute, National Laboratory, Environmental Genomics and Systems
Biology, 1 Cyclotron Road, Berkeley, CA, 94720, USA
3 current address: Institute for Plant and Microbial Biology, University of Zurich,
8008 Zurich, Switzerland
2022-12-08 | MSV000090869 | GNPS
Project description:Microbial communities from bioreactor (seeded with sewage sludge) at Lawrence Berkeley National Lab, California, USA - Biofuel Metagenome 8
| PRJNA384660 | ENA
Project description:Microbial communities from bioreactor (seeded with sewage sludge) at Lawrence Berkeley National Lab, California, USA - Biofuel Metagenome 9
| PRJNA384661 | ENA