Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Halo_itraq12

ABSTRACT: Proteins harvested from cultures recovering from 0Gy (control) or 2500Gy (experimental) of gamma irradiation stress and labeled with iTRAQ, multiplex sample #12 with three time points 30, 40, 60 min during recovery compared against common reference; Whitehead et al., 2006 Mol Syst Biol. 2(47). Replicate of #11.

OTHER RELATED OMICS DATASETS IN: PRJNA96059PRD000496

INSTRUMENT(S): ABI QSTAR

ORGANISM(S): Halobacterium Nrc-1 (halobacterium)

SUBMITTER: Kenia Whitehead and Nitin Baliga

PROVIDER: PAe000259 | PeptideAtlas | 2006-12-31

REPOSITORIES: PeptideAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PAe000259_257_search.params.tar.gz	Other
	PAe000259_257_searchdatabase_sequest.fasta	Fasta
	PAe000259_257_sequest.params	Other
	PAe000259_RAW.tar	Raw
	PAe000259_README	Other

Items per page:

1 - 5 of 11

Publications

An integrated systems approach for understanding cellular responses to gamma radiation.

Whitehead Kenia K Kish Adrienne A Pan Min M Kaur Amardeep A Reiss David J DJ King Nichole N Hohmann Laura L DiRuggiero Jocelyne J Baliga Nitin S NS

Molecular systems biology 20060912

Cellular response to stress entails complex mRNA and protein abundance changes, which translate into physiological adjustments to maintain homeostasis as well as to repair and minimize damage to cellular components. We have characterized the response of the halophilic archaeon Halobacterium salinarum NRC-1 to (60)Co ionizing gamma radiation in an effort to understand the correlation between genetic information processing and physiological change. The physiological response model we have construc ...[more]

PMID: 16969339

Similar Datasets

Interaction of soil amoeba Protostelium aurantium with three pathogenic yeasts Candida spp. (here: C. parapsilosis)

Project description:We investigated different escape and defense strategies of Candida parapsilosis against the natural fungivorous predator Protostelium aurantium using dual RNA-Seq. Trophozoites of the amoeba Protostelium aurantium were fed with C. parapsilosis and samples for RNA isolation were taken at time points 0 min (control), 30 min and 60 min. At indicated time points samples were shock frozen and used for RNA isolation. C. parapsilosis underwent rapid predation and intracellular killing of the yeast

2018-09-01 | GSE116534 | GEO

2D-LC/MS/MS analysis of Escherichia coli during exposure an abrupt downshift in water activity

Project description:2D-LC/MS/MS analysis was used to examine time-dependent changes in proteome of E. coli O157:H7 strain Sakai upon an abrupt downshift in water activity (aw) (i.e., from aw 0.993 to aw 0.967) at a constant temperature of 35°C. Bacterial cells were harvested before hyperosmotic shift, and 0 (i.e. immediately after the shift), 30, 80, and 310 min after the shift. It also should be noted that these time points were chosen with the aims to characterize the physiology of E. coli during dynamic changes in growth kinetics induced by an abrupt downshift in water activity. Specifically, the samples taken at time 0 and 30 min were obtained during the period in which the loss of cell culturability was observed, whereas the samples at time 80 and 310 min respectively reflected the physiological state of E. coli during the ‘recovery’ period and during growth after the shift.

2014-04-14 | PXD000541 | Pride

Interaction of soil amoeba Protostelium aurantium with three pathogenic yeasts Candida spp. (here: C. albicans and C. glabrata)

Project description:We investigated different escape and defense strategies of Candida glabrata and Candida albicans against the natural fungivorous predator Protostelium aurantium using dual RNA-Seq. While C. albicans was found to be very succesfull in preventing from amoeba recognition, C. glabrata in turn, was rapidly taken up but remained undigested with a comparably low transcriptional activity. Trophozoites of the amoeba Protostelium aurantium were fed seperately with the two fungal species and samples for RNA isolation were taken at time points 0 min (control), 30 min and 60 min. At indicated time points samples were shock frozen and used for RNA isolation. Samples for RNAseq were taken at time points 0 min (control), 30 min and 60 min. RNA samples from identical timepoints for C. albicans and C. glabrata were pooled for RNA sequencing. We investigated different escape and defense strategies of Candida spp. against natural fungivorous predator. While C. parapsilosis underwent rapid predation and intracellular killing of the yeast, C. albicans was found to be very succesfull in preventing from amoeba recognition. C. glabrata in turn, was rapidly taken up but remained undigested with a comparably low transcriptional activity.

2018-09-01 | GSE116533 | GEO

Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit

Project description:Escherichia coli strain MG1655 was grown in a Zn-depleted custom-built chemostat. Culture volume (120 ml), temperature (37 oC) and stirring speed (440 rpm) were maintained. Steady state values for pH and OD600 were 6.9 and 0.6, respectively. Chemostats were grown for 50 h to allow five culture volumes to pass through the vessel and allow an apparent (pseudo-)steady state to be reached. At this point, ZnSO4.7H2O in water was added to a final concentration of 0.2 M in the chemostat. A 10 ml sample of culture was taken using a polypropylene pipette tip immediately prior to Zn addition and 2.5, 7, 10 and 30 min after addition. Samples were harvested into RNAprotect and total RNA was purified using Qiagen’s RNeasy Mini kit (using the supplier’s protocol) prior to use in microarray analysis. A control experiment was also carried out in which water was added. Biological experiments were carried out twice (i.e. control (water added) and experiment (ZnSO4 added) chemostats were grown separately twice), and a dye swap performed for each experiment, providing at least two technical repeats for each of the two biological repeats at all five time points. Slides were analysed so that time points “with Zn” were compared to the same time point “without Zn” (e.g. 30 min after Zn was added was compared to 30 min after water being added).

2011-12-01 | GSE26187 | GEO

2D-LC/MS/MS analysis of Escherichia coli during exposure to an abrupt temperature downshift

Project description:2D-LC/MS/MS analysis was used to examine time-dependent changes in proteome of E. coli O157:H7 strain Sakai upon an abrupt downshift in temperature (i.e., from 35°C to 14°C). Cell cultures were harvested at 30, 90, 160, and 330 min post-temperature downshift. It also should be noted that these time points were chosen with the aims to characterize the physiology of E. coli during dynamic changes in growth kinetics induced by an abrupt temperature downshift. Specifically, the samples taken at time 30 and 90 min were obtained during adaptation period, whereas the samples at time 160 and 330 min reflected the physiological state of E. coli during growth after the shift. MS/MS data obtained from each protein sample were processed by the Computational Proteomics Analysis System (CPAS), a web-based system built on the LabKey Server (v9.1, released 02.04.2009). The experimental mass spectra produced were subjected to a semi-tryptic search against the combined databases of E. coli O157:H7 Sakai (5,318 entries in total) downloaded from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/, downloaded 25.11.2008) using X!Tandem v2007.07.01. These databases included the E. coli O157:H7 Sakai database (5230 entries, NC_002695.fasta) and two E. coli O157:H7 Sakai plasmid databases, plasmid pO157 (85 entries, NC_002128.fasta) and plasmid pOSAK1 (three entries, NC_002127.fasta). The parameters for the database search were as follows: mass tolerance for precursor and fragment ions: 10 ppm and 0.5 Da, respectively; fixed modification: cysteine cabamidomethylation (+57 Da); and no variable modifications. The search results were then analyzed using the PeptideProphet and ProteinProphet algorithms from the Trans Proteomic Pipeline v3.4.2. All peptide and protein identifications were accepted at PeptideProphet and ProteinProphet of ≥0.9, corresponding to a theoretical error rate of ≤2%.

2019-11-25 | PXD000573 | Pride

RNA-seq of Bacillus subtilis WT W168 treated with the antimicrobial peptide YydF (0.5µM) compared to untreated control

Project description:To obtain global cellular response of Bacillus subtilis WT W168 against the intrinsically produced antimicrobial peptide YydF, we performed RNA-seq experiments. For this, we synthesized YydF, extrinsically added 0.5µM to logarithmic phase growing cells and harvested cells after 10 min exposure. Experiments were performed in triplicates and non-induced Bacillus subtilis WT W168 was used as reference condition.

2019-12-16 | GSE140605 | GEO

3′-seq of Saccharomyces cerevisiae grown in eight different conditions

Project description:Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) was grown in YPD medium. For control conditions, cells were grown in mid-log phase at 30°C for 20 min or 2 hours. Stress conditions were heat shock (37°C for 20 min), diauxic shift (harvested at 2 hours after glucose depletion), DNA damage (harvested after 2 hours of treatment with 5 µg/ml 4-nitroquinoline 1-oxide (Sigma)). Moreover, four conditions of the yeast metabolic cycle were analyzed. S. cerevisiae strain CEN.PK (MATa URA3 TRP1 LEU2 HIS3 MAL2-8C SUC2) was used and cultivated as described elsewhere (Nocetti and Whitehouse, Genes Dev, 2016). The period of metabolic oscillation was approximately 3.2 h. Cells were harvested at 16, 32, 48, and 60 min from the start of each cycle for one oxidative, two reductive/building, and one reductive/charging phase points. Total RNA from each sample was extracted by the hot phenol method and used for library preparation. 3′-seq libraries were prepared as described previously (Lianoglou et al., Genes Dev, 2013). Each condition was sequenced in three biological replicates. The 27 individual libraries were pooled and subjected to sequencing with HiSeq with SR50 at the Integrated Genomics Operation (MSKCC).

2023-09-30 | GSE213720 | GEO

Halobacterium NRC-1, EMS Stress Response

Project description:100mM EMS was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of EMS for 30 minutes, cultures were spun down and pellets were re-suspended in same volume of GN101 media. Cultures were then harvested by centrifugation and pellets were snap frozen on a dry-ice ethanol bath. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. 16 samples (8 samples from EMS perturbed and 8 non-perturbed controls) were analyzed on replicate arrays (dye-flips) all against the same standard reference sample.

2010-05-27 | E-GEOD-7609 | biostudies-arrayexpress

Cytoreduction Followed by Normothermic Versus Hyperthermic Intraperitoneal Intraoperative Chemoperfusion (HIPEC): a Study in Peritoneal Carcinomatosis

Project description:Peritoneal carcinomatosis from appendix or colon (large bowel) cancer is treated in suitable patients with surgery followed by instillation of heated chemotherapy inside the abdominal cavity. This procedure is termed ‘Hyperthermic intraoperative Peritoneal Chemoperfusion’ or HIPEC. Many center perform HIPEC with high dose oxaliplatin, a standard chemotherapy drug active against colon cancer, administered during 30 minutes at 41°C. The hypothesis of this study is, that chemoperfusion at normal (37.5°C) temperature but longer duration (90 minutes) may be safer and at least as efficient. Patients will be treated with one of three possible HIPEC regimens using oxaliplatin: high dose, 30 min, 41°C; high dose, 30 min, 37.5°C; or low dose, 90 min, 37.5°C. The outcome parameters are pharmacokinetic and pharmacodynamic: using specialized techniques, tissue penetration of chemotherapy and cancer cell kill effects will be compared in order to establish the safest and most active HIPEC regimen.

| 2123613 | ecrin-mdr-crc

Mating response - six alpha factor concentrations (0.06, 0.2, 0.6, 6, 60 and 600 nM)

Project description:We examined the mating response of W303 bar1delta a-type cells to six alpha-factor concentrations (0.06, 0.2, 0.6, 6, 60 and 600 nM). In each alpha factor concentration between five to seven time points were collected. The time points in all experiments (except for concentration 600 nM were time point 15 min was omitted) were 5, 15, 30, 60, and 90 min. In some of the concentrations also time points 120 and 150 min were considered. The expression of cells before and after addition of alpha-factor were compared using S. cerevisiae cDNA microarrays, in all experiments the same sample before adding alpha factor was used as a control. Keywords: yeast mating response, comparison among alpha factor concentrations

2007-09-11 | GSE8982 | GEO