Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1235292 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32680300_1.fastq.gz | Fastqsanger.gz | |||
| SRR32680300_2.fastq.gz | Fastqsanger.gz | |||
| SRR32680400_1.fastq.gz | Fastqsanger.gz | |||
| SRR32680400_2.fastq.gz | Fastqsanger.gz | |||
| SRR32680500_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1536 |
Similar Datasets
Project description:Survey of relative gene expression profiles in larvae, pupae, and midguts and fatbodies of teneral, unfed, and fed adult mountain pine beetles from western Nevada, USA.
2009-08-29 | GSE17858 | GEO
Project description:We sequenced mRNA from brain samples of 20 captive Swainson's thrushes. 10 were from California, belonging to the coastal subspecies, and 10 were from Alaska, belonging to the inland subspecies.
2016-12-15 | GSE87549 | GEO
Project description:Local adaptation can play a fundamental role in the isolation of populations. While less well-studied than differentiation in sequence variation, changes in transcriptional variation during speciation also are fundamental to the evolutionary process. Drosophila mojavensis offers an unprecedented opportunity to examine the role of transcriptional differentiation in local adaptation. Drosophila mojavensis is a cactophilic fly composed of four ecologically distinct subspecies that inhabit the deserts of western North America. Each of the four subspecies utilizes necrotic tissue of different cactus host species characterized by distinct chemical profiles. The subspecies in Baja California, Mexico uses Stenocereus gummosus (Agria), in mainland Sonora it uses S. thurberi (Organ Pipe), in the Mojave Desert the host is Ferocactus cylindraceus (Red Barrel) and in Santa Catalina Island, USA, Opuntia littoralis (Prickly Pear) is the host. In this chapter we examine how the adaptation to the different environmental conditions across the four subspecies have shaped their transcriptional profiles. Using complete D. mojavensis genome microarrays we examined the transcriptome of third instar larvae from all four subspecies reared in standard laboratory media free of necrotic cactus-derived compounds. This experimental strategy focused on differences between constitutively expressed genes and not genes induced by necrotic cactus-derived compounds. The subspecies exhibited significant differential expression of genes that likely underlie the adaptation to different cactus hosts, such as detoxification genes (Glutathione S-transferases, Cytochrome P450s and UDP-Glycosyltransferases) and chemosensory genes (Odorant Receptors, Gustatory Receptors and Odorant Binding Proteins). Dataset from Matzkin, L. M. and Markow, T.A. Transcriptional differentiation across the four cactus host races of Drosophila mojavensis. In Speciation: Natural Processes, Genetics and Biodiversity. Edited by Michalak, P. Nova Science Publishers, Inc.
2015-01-01 | GSE41155 | GEO
Project description:This dataset contains raw spectral data captured from sorghum roots collected from four Sorghum bicolor L. Moench genotypes grown in an arid field setting in Maricopa, Arizona in water-replete and water-limited conditions. We used these data to examine the root metabolome of field-grown sorghum in Arizona, USA, and related metabolomic data to microbial responses to stress.
2024-10-15 | MSV000096099 | MassIVE
Project description:The following cell lines were used for this study: Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) derived from 5 human (Coriell YRI, NIGMS Human Genetic Cell Repository, GM18505, GM18507, GM18516, GM19193, GM19204), and 5 chimpanzee (Pan troglodytes) individuals (New Iberia Research Center: Min 18358, Min 18359; Coriell/IPBIR: NS03659, NS04973, Arizona State University, Pt91), and rhesus Herpesvirus papio transformed LCLs from 5 rhesus macaque (Macaca mulatta) individuals (Harvard Medical School, NEPRC: 150-99, R181-96, R249-97, 265-95, R290-96). Cells were maintained at identical conditions of 37° with 5% CO2 in RPMI media with 15% FBS, supplemented with 2 mM L-glutamate, 100 IU/ml penicillin, and 100 ug/ml streptomycin. Internal standard LCL (Coriell YRI, NIGMS Human Genetic Cell Repository, GM19238) was grown in RPMI minus L-Lysine and L-Arginine, 15% dialyzed FBS, and L-13C615N4-arginine (Arg-10) and L-13C615N2-lysine (Lys-8) (Cambridge Isotopes, Andover, MA, USA) supplemented with 2 mM L-glutamate, 100 IU/ml penicillin, and 100 ug/ml streptomycin under identical conditions as the unlabeled LCLs. The internal standard LCL was grown for 6 doublings to assure complete SILAC label incorporation. Complete label incorporation was verified by analyzing the protein lysate from the labeled LCL alone by high-resolution LC-MS/MS. LCLs were washed in PBS three times and then lysed using the UPX Universal Protein Extraction Kit (Expedeon Inc., San Diego, CA, USA). Protein quantitation was performed using the Qubit fluorometry assay (Invitrogen, Carlsbad California, USA) and the reducing agent-compatible (RAC) version of the BCA Protein Assay (Thermo Scientific, Waltham, Massachusetts, USA). 12ug of each sample was combined with 12ug of the SILAC labeled lysate from human LCL GM19238. Note that the SILAC lysate was prepared once and used as an internal standard through the quantification of the 15 cell lines. 24ug of each combined sample was then processed by SDS-PAGE using a 4-12% Bis Tris NuPage mini-gel (Invitrogen, Carlsbad California, USA). Calibration was with Thermo PageRuler broad range markers. Each of 40 gel segments were processed by in-gel digestion using a ProGest robot (DigiLab, Marlborough, MA, USA) with the following protocol: wash with 25mM ammonium bicarbonate followed by acetonitrile, reduce with 10mM dithiothreitol at 60°C followed by alkylation with 50mM iodoacetamide at room temperature, digest with trypsin (Promega, Madison, WI, USA) at 37°C for 4h, and quench with formic acid. The supernatant was analyzed directly without further processing. Each of gel digest was analyzed by nano-LC/MS/MS with a Waters NanoAcquity HPLC system interfaced to a ThermoFisher LTQ-Orbitrap Velos Pro. Peptides were loaded on a trapping column and eluted over a 75um analytical column at 350nL/min using a 1-hour LC gradient. Both columns were packed with Jupiter Proteo resin (Phenomenex, Torrance, California, USA). The mass spectrometer was operated in data-dependent mode, with MS performed in the Orbitrap at 60,000 FWHM resolution and MS/MS performed in the LTQ. The fifteen most abundant ions were selected for MS/MS. Low-level data analysis was performed using the open-source proteomics software tool PVIEW (Release December 23, 2012; http://compbio.cs.princeton.edu/pview). As input to PVIEW, we generated in silico translations of coding genes from the UCSC Genome Browser database based on gene models from build hg19 of the human genome. Each protein sequence entry retained the corresponding Ensembl gene identifier and gene symbol. Database searches were performed using +-4 p.p.m. MS1 tolerance and an MS2 window tolerance of +-0.5 Da. Up to 2 missed tryptic cleavages were allowed during search. Carboxyamidomethylation of cysteine was used as fixed modification. Up to two methionine oxidations were allowed as variable modifications of a tryptic peptide. Peptide spectrum matches were obtained at a stringent false discovery rate (FDR) of 1%. We used the median log2(sample/standard) ratio across all independent quantifications of a protein (distinct peptides including duplicate peptide measurements across fractions and for differing charge states). Note that use of the hg19 database was sufficient as SILAC pairs as the expected isotope shift used for quantification were only present for peptides that that had the same underlying sequence in the human internal standard line. Associated RNA-seq data have been deposited to GEO with accession number GSE49682.
2013-10-01 | PXD000419 | Pride
Project description:Please Note, if a password is required, please try "a", the generic password for Massive.
These data are in support of the manuscript:
Post-translational Modifications of Endogenous Tau in Wildtype and Human Amyloid Precursor Protein Transgenic Mice
Meaghan Morris*a,b, Giselle M. Knudsen*c, Sumihiro Maedaa,d, Jonathan C. Trinidadc, Alexandra Ianoviciuc, Alma L. Burlingamec, Lennart Muckea,d
aGladstone Institute of Neurological Disease, San Francisco, California 94158, USA
bBiochemistry, Cellular and Molecular Biology Graduate Program, Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
cMass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
dDepartment of Neurology, University of California, San Francisco, California 94158, USA
*These authors contributed equally to this work
2014-07-30 | MSV000078796 | MassIVE
Project description:This experiment set includes 64 arrays representing 26 serovars and strains of Salmonella spp. including many representatives of subspecies I, Arizona from subsp. IIIa, and S. bongori from subsp. V. The genomic DNA from all strains were labeled with Cy5 and hybridized against an equal amount (1.5 ug) of S. typhimurium SL1344 reference genomic DNA that was labeled with Cy3, all on an S. typhimurium SL1344 spotted DNA microarray. Most of the arrays are present in triplicate to account for variability in probe generation, hybridization, and slide quality. Several are represented in duplicate, and a few without any replicates. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-11-04 | GSE3564 | GEO
Project description:In this experiment we tested the transcriptome of transgenic Arabidopsis seedlings (5-day-old) constitutively expressing the zinc-finger protein Zat12 (At5g59820) under the control of the 35S-CaMV promoter (Zat12). The transcriptome of these seedlings was compared to that of wild type seedlings grown under the same conditions (WT) and to that of wild type seedlings grown under the same conditions and subjected to a hydrogen peroxide stress (WT+H2O2). Hydrogen peroxide treatment was performed by applying 20 mM hydrogen peroxide for 1 hour. In parallel to these experiments transgenic plants expressing Zat12 were subjected to a similar hydrogen peroxide stress (Zat12+H2O2). All treatments were performed with similar size and age seedlings grown in liquid culture (MS) and sampled at the same time as described by Davletova et al., 2005. Experimenter name = Ron Mittler Experimenter phone = 1-775-784-1384 Experimenter fax = 1-775-784-1650 Experimenter department = Dept. of Biochemistry Experimenter institute = University of Nevada Experimenter address = MS200 Experimenter address = Reno Experimenter address = Nevada Experimenter zip/postal_code = 89557 Experimenter country = USA Keywords: genetic_modification_design; stimulus_or_stress_design
2006-08-15 | GSE5530 | GEO