Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq study of the response of the diatom Leptocylindrus aporus to changing temperature conditions.

ABSTRACT: The goal of the experiment was to compare the behavior and responses of a warm water diatom species in three different temperatures, low, intermediate and high, with the final aim of investigating possible intraspecific variability and better understanding the physiological plasticity and/or adaptation of diatoms to a wide range of conditions. Three different strains were used as replicates, B651,1A1,3A6. They were isolated from sea surface waters at the LTER-MC site (40°48.5’N, 14°15’E) in the Gulf of Naples on 21/08/2010, 20/12/2013 and 28/01/2014 respectively and grown in cultures. All three strains were acclimated to 13°C, 19°C and 26°C at a light intensity of 100 μmol photons m-2 sec-1 and a photoperiod of L:D, 12:12 and grown to a final concentration of 50,000 cells/ml ensuring they were still at exponential phase.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Leptocylindrus aporus

SUBMITTER: Mariella Ferrante

PROVIDER: E-MTAB-8596 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chip-chip from undifferentiated and neuron-differentiated hMSCs cells with EZH2

Project description:EZH2 plays an important role in stem cell renewal and maintenance by inducing gene silencing via its histone methyltransferase activity. Previously, we showed EZH2 downregulation markedly enhances neuron differentiation of human mesenchymal stem cells (hMSCs). To understand how EZH2 regulates neuron differentiation of hMSCs, we wanted to identify the target genes of EZH2. For this reasons we performed ChIP-on-chip experiments using specific EZH2 antibodies followed by a human promoter array for the whole human genome. The 3A6-hMSCs were differentiated into neuron for 5 days, and then 109 cells were harvested for the ChIP-on-chip assay. The procedure was based on the manufacturer's instructions (NimbleGen).

2012-12-05 | E-GEOD-42686 | biostudies-arrayexpress

Hepatic transcriptomic alterations for polybrominated diphenyl ether 47 (PBDE47) after 5-day exposure in rats

Project description:To identify liver transcripts differentially expressed due to treatment with polybrominated diphenyl ether 47 (PBDE47), we collected RNA from male Harlan Sprague Dawley rats exposed to 0, 0.0485, 0.485, 4.85, 48.5 or 485 mg/kg PBDE47, 5 days after exposure for animals 7 weeks of age. These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array. A total of 44,28,111,999, and 3195 gene transcripts were differentially expressed due to PBDE47 treatment after exposure to 0.0485, 0.485, 4.85, 48.5 or 485 mg/kg PBDE47 (false discovery rate (FDR) < 0.05).

2020-07-15 | GSE153360 | GEO

Homo sapiens immortalized MSCs: 3A6

Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs. One-condition experment, gene expression of 3A6

2010-09-25 | E-GEOD-24338 | biostudies-arrayexpress

RNA-seq analysis of mouse hippocampal gene expression changes after Gulf War toxicant exposure

Project description:Differentially expressed genes may provide insight into the underlying mechanisms of Gulf War Illness involved in neurodegeneration.

2021-07-27 | GSE180786 | GEO

A genetic platform to investigate the functions of bacterial drug efflux pumps

Project description:Efflux pumps are a significant challenge for the development of new antibacterial agents. Overcoming efflux requires an in-depth understanding of efflux pump functions, substrate specificities, and the development of inhibitors. However, the complexities of drug efflux networks have limited such studies. To address these challenges, we report the generation of Efflux KnockOut-35 (EKO-35), a highly susceptible Escherichia coli strain lacking 35 efflux pumps. We demonstrate the utility of this strain by constructing an efflux platform consisting of strains individually expressing genes encoding efflux pumps forming tripartite complexes with the outer membrane channel TolC. This platform was profiled against a curated diverse compound collection, which enabled us to define physicochemical properties that contribute to transport. We also show the E. coli drug efflux network is conditionally essential for growth, and that the platform can be used to investigate efflux pump inhibitor specificities and also efflux pump interplay. We believe EKO-35 and the efflux platform will have widespread application for the study of drug efflux.

2022-08-31 | PXD033975 | Pride

Transcription profiling of blood from Gulf War Illness sufferers and control veterans before and after exercise

Project description:This pilot study enrolled 9 GWI (Gulf War Illness) cases identified from the Department of Veterans Affairs GWI registry, and 11 sedentary control veterans who had not been deployed to the Persian Gulf and were matched to cases by sex, body mass index (BMI) and age.<br>We exposed GWI patients and matched controls to an exercise challenge to explore differences in immune cell function measured by classic immune assays and gene expression profiling.

2009-02-24 | E-MEXP-2069 | biostudies-arrayexpress

Toxic Exposure of Pyridostigmine Bromide Chronically Impairs Colonic Motility Via Low Grade Enteric Neuroinflammation

Project description:Combat veterans from the Persian Gulf War have unexplained yet persistent impairment in colonic motility due to combat-related toxic exposures. Central to Gulf War-related toxic exposures was the unmitigated ingestion of Pyridostigmine bromide (PB). We previously developed a Gulf War Illness (GWI) mouse model, where acute PB exposure led to immediate disruptions in colonic motility. Here, we explore mechanisms by which acute enteric neuroinflammation produces peristent impairment in colonic motility. GWI mice were exposed to PB transiently, and allowed to recover with no exposures for 1 month. GWI mice had significantly increased amplitudes of colonic contraction and diminished nerve-stimulated colonic relaxation, compared to naive controls. Immunohistological characterization demonstrated persistent chronic damage in enteric neuronal network integrity, accompanied by a significant imbalance in excitatory and inhibitory motor neuronal populations. Inflammatory CD40+ tissue- resident macrophages were identified with enteric neural stem cells in GWI colons, with an increase in secreted inflammatory cytokines. Unbiased transcriptomic analysis corroborated peristent low grade enteric neuroinflammation, overall resulting in impaired repair and regeneration of neural circuity in GWI. Our learnings can be leveraged to design new regenerative therapies for Gulf War veterans, and broadly impact our understanding of severeal inflammatory disorders of the gut.

2024-09-07 | GSE276269 | GEO

A systematic proteogenomic approach to deciphering of the missing proteins: the example of newly uncovered NHERF1 function associated with human reproductive disorder

Project description:We propose and demonstrate a systematic approach designed to combine stringent criteria for claims of missing protein (MP) identification with extensive annotation as critical components of the discovery and functional validation of MPs.

2018-01-05 | PXD004723 | Pride

TEF-seq/NET-seq applied to factors Rpb3, Paf1, Spt6, Spt16, Cet1, Pcf11, Ssu72, Set2

Project description:Here we adapt native elongating transcript sequencing (NET-seq) to develop transcription elongation factor associated nascent elongating transcript sequencing (TEF-seq). In this the RNA polymerase II (Pol2) transcription elongation complex (TEC) is immunoprecipitated via associated transcription elongation factors (TEFs). Sequencing from the 3' end of the Pol2-associated nascent transcript shows the position of the final incorporated nucleotide giving strand-specific, single nucleotide resolution maps of the level of TEF association with Pol2 during transcription.

2021-01-18 | E-MTAB-4568 | biostudies-arrayexpress

Homo sapiens immortalized MSCs: KP vs. 3A6

Project description:Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs. Two-condition experiment, KP MSCs vs. 3A6 MSCs.

2011-08-24 | E-GEOD-23936 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data