Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-enabled studies of anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

ABSTRACT: Investigation of whole genome gene expression level changes in anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans Here we report on a study to identify genes associated with nitrate-dependent Fe(II) oxidation by whole-genome transcriptional (microarray) assays including the use of FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions. A 25 chip study using total RNA recovered from wild-type T. denitrificans was cultivated at 30oC under strictly anaerobic conditions with growth medium that contained 20 mM thiosulfate, 20 mM nitrate, and 30 mM bicarbonate (pH ~7) and exposed to 8 treatments. Each chip measures the expression level of 2832 ORFs with N 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

ORGANISM(S): Thiobacillus denitrificans ATCC 25259

SUBMITTER: Anu Chakicherla

PROVIDER: E-GEOD-46339 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Growth rate-corrected (GR) dose-response metrics across a panel of 71 breast cancer cell lines treated with a library of small molecule and antibody perturbagens. Dataset 2 of 4: Calculated dose-response metrics.

Project description: Not available

2017-03-14 | LDS-1363 | LINCS

Growth rate-corrected (GR) dose-response metric signatures across a panel of 71 breast cancer cell lines treated with a library of small molecule and antibody perturbagens. Dataset 4 of 4: Median, upper quartile, and lower quartile GR metrics per perturbagen class.

Project description: Not available

2017-02-01 | LDS-1365 | LINCS

Growth rate-corrected (GR) dose-response metric signatures across a panel of 71 breast cancer cell lines treated with a library of small molecule and antibody perturbagens. Dataset 3 of 4: Median, upper quartile, and lower quartile GR metrics per perturbagen.

Project description: Not available

2017-07-20 | LDS-1364 | LINCS

Growth rate-corrected (GR) dose-response metrics across a panel of 71 breast cancer cell lines treated with a library of small molecule and antibody perturbagens. Dataset 1 of 4: Relative cell counts and normalized growth rate inhibition values across technical replicates.

Project description: Not available

2017-02-01 | LDS-1362 | LINCS

Comparison of Gametocyte producer 3D7-A subclone E5 to the gametotcyte nonprodcer strain F12 and pfap2-g deletion mutant

Project description:Identify differentially expressed genes across the 48h intraerythrocytic development cycle of gametocyte non-producers of P. falcuparum two-color comparison to a common labeled reference pool

2013-11-06 | E-GEOD-52030 | biostudies-arrayexpress

Constitutive expression of Medicago truncatula NRT1 PTR FAMILY 1.7 enhances growth in Arabidopsis thaliana

Project description:To gain insight into the molecular mechanisms underlying the increased growth of Col-0:MtNPF1.7 CE plants compared to WT, leaves from plants grown for 21 days on defined media were subjected to transcript profiling using the Affymetrix Arabidopsis ATH1 microarray. We tested gene expression from plants grown at 0.1 mM nitrate and at 10 mM nitrate. The 0.1 mM nitrate concentration is below MtNPF1.7’s Km and at that nitrate concentration, large growth differences between Col-0:MtNPF1.7 CE and wild-type Col-0 plants were observed, while 10 mM nitrate is well above MtNPF1.7’s Km, where fewer differences in growth were seen. Three independent biological replicates were collected.

2021-06-26 | E-MTAB-3750 | biostudies-arrayexpress

Genome-wide DNA methylation profiling reveals epigenetic changes in the rat nucleus accumbens associated with cross-generational effects of adolescent THC exposure

Project description:Drug exposure during critical periods of development is known to have lasting effects, increasing one’s risk for developing mental health disorders. Emerging evidence has also indicated the possibility for drug exposure to even impact subsequent generations. Our previous work demonstrated that adolescent exposure to Δ9-tetrahydrocannabinol (THC), the main psychoactive component of marijuana (Cannabis sativa), in a Long-Evans rat model affects reward-related behavior and gene regulation in the subsequent (F1) generation unexposed to the drug. Questions, however, remained regarding potential epigenetic consequences. In the current study, using the same rat model, we employed Enhanced Reduced Representation Bisulfite Sequencing to interrogate the epigenome of the nucleus accumbens, a key brain area involved in reward processing. This analysis compared 16 animals with parental-THC exposure and 16 without to characterize relevant systems-level changes in DNA methylation. We identified 1,027 differentially methylated regions (DMRs) associated with parental THC exposure in F1 adults, each represented by multiple CpGs. These DMRs fell predominantly within introns, exons, and intergenic intervals, while showing a significant depletion in gene promoters. From these, we identified a network of DMR-associated genes involved in glutamatergic synaptic regulation, which also exhibited altered mRNA expression in the nucleus accumbens. These data provide novel insight into drug-related cross-generational epigenetic effects, and serve as a useful resource for investigators to explore novel neurobiological systems underlying drug abuse vulnerability. Study consisted of a total of 32 F1 individuals (Long-Evan rats); 16 animals (8 female, 8 male) were offspring from THC-exposed parents, and the remaining 16 animals (8 female, 8 male) were offspring from saline-exposed parents ("controls"; "VEH-exposed").

2015-06-19 | E-GEOD-69984 | biostudies-arrayexpress

Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin

Project description:We report genome-wide detection of long noncoding RNA (lncRNA) generate by Pol V in transcriptional gene silencing in Arabidopsis thaliana. We further show that most of these transcripts are bound by AGO4. RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) RNA immunoprecipitation with an anti-AGO4 antibody was performed in one biological replicate and included Col-0, nrpe1, and ago4-1; RNA immunoprecipitation with an anti-NRPE1 (largest subunit of Pol V) was performed in two replicates; replicate 1 included Col-0 and nrpe1, replicated two included Col-0, nrpe1, ago4-1, and idn2-1

2016-10-24 | E-GEOD-70290 | biostudies-arrayexpress

Effect of hypoxia on Mycobacterium tuberculosis-host phagocyte interactions

Project description:Mtb appears to have developed specialized biomolecular infrastructure to survive and persist within granulomas, where it is subjected to a diverse set of stress conditions. One of these stress conditions is hypoxia. We hypothesized that host cell response is radically altered with hypoxia stressed Mtb and designed in-vitro experiments to study this phenomenon. Hypoxia-stressed as well as aerobically grown Mtb were used to infect rhesus macaque bone marrow derived macrophages (Rh-BMDMs) and the host global transcriptional response compared. Using 4 x44 k Agilent arrays specific for rhesus macaque genome, we tested in biological duplicate the effect of aerogically grown Mtb on rhesus macaque BMDMs and compared this to the corresponding effect of the hypoxia-conditioned Mtb on rhesus macaque BMDMs

2013-05-22 | E-GEOD-47163 | biostudies-arrayexpress

Gill Transcriptomic Responses to Toxin-producing Alga Prymnesium parvum in Rainbow Trout

Project description:Prymnesium parvum is regarded as one of the most notorious harmful algal bloom (HAB) species worldwide. In recent years, it has frequently formed toxic blooms in coastal and brackish waters of America, Europe, Australia, Africa and Asia, causing large-scale mortalities of wild and cultured fish and other gill-breathing animals. In the last decade, blooms of P. parvum have expanded to inland fresh waters in the USA, presumably due to changes in environmental conditions. The aim of the experiment was to establish the gill transcriptomic responses to P. parvum in rainbow trout. We used 2 different concentrations of P. parvum and identified fish with low and moderate responses to the algae. Based on the dose of and the fish response, fish were classified into 4 groups with high exposure/moderate response (HM), high exposure/low response (HL), low exposure/low response (LL) and control group (C) with no exposure/no response. Gene expression profiling of the gill tissue was performed using a microarray platform developed and validated for rainbow trout.

2021-11-10 | E-MTAB-10541 | 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