Browse
Submit Data
Databases
API
Help

Dataset Information

349 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complementary metaproteomic approaches to assess marine bacteriopankton response towards algal bloom

ABSTRACT: In this project, the metaproteome of the marine bacterioplankton was analyzed to assess its respone towards an algal bloom in the southern North Sea in spring 2010. Proteins were extracted applying two different methods: (i) applying chemical cell lysis using trifluoroethanol in combination with in-solution digest and (ii) mechanical cell lysis applying bead beating, SDS-PAGE prefractionation and in-gel digest. Both samples were analyzed by nanoLC and ESI-iontrap MS. In case of the TFE lysis samples, also nanoLC-MALDI-TOF MS was applied.

INSTRUMENT(S): amaZon Speed ETD

ORGANISM(S): Environmental Samples

SUBMITTER: Lars Wöhlbrand

LAB HEAD: Lars Wöhlbrand

PROVIDER: PXD004944 | Pride | 2017-04-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	BBGeLC_St10_A.pdf	Pdf
	BBGeLC_St10_B.pdf	Pdf
	BBGeLC_St10_C.pdf	Pdf
	BBGeLC_St3_A.pdf	Pdf
	BBGeLC_St3_B.pdf	Pdf

Items per page:

1 - 5 of 43

Publications

Complementary Metaproteomic Approaches to Assess the Bacterioplankton Response toward a Phytoplankton Spring Bloom in the Southern North Sea.

Wöhlbrand Lars L Wemheuer Bernd B Feenders Christoph C Ruppersberg Hanna S HS Hinrichs Christina C Blasius Bernd B Daniel Rolf R Rabus Ralf R

Frontiers in microbiology 20170324

Annually recurring phytoplankton spring blooms are characteristic of temperate coastal shelf seas. During these blooms, environmental conditions, including nutrient availability, differ considerably from non-bloom conditions, affecting the entire ecosystem including the bacterioplankton. Accordingly, the emerging ecological niches during bloom transition are occupied by different bacterial populations, with <i>Roseobacter</i> RCA cluster and SAR92 clade members exhibiting high metabolic activity ...[more]

PMID: 28392779

Similar Datasets

Global analysis of mRNA expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE

Project description:Human prostate CWR22 OT-tumor cells were prospectively purified for expression of various stem cell markers (TRA-1-60/CD151/CD166/EpCAM/CD44/α2-Integrin). Unsorted total tumor cells or the additional marker positive cells that do not manifest stem-like characteristics were used as control. All these cells were subjected to molecular profiling of total RNA expression and the fold change data are tabulated according to S/TFE of the purified cells in relation to their control. Notes: Low S/TFE = Low sphere and tumor forming efficiency; Moderate S/TFE = Moderate sphere and tumor forming efficiency; High S/TFE = High sphere and tumor forming efficiency; FDR* = False Discovery Rate; FC = Fold Change; Signal = Average Expression Signal Level. Low-S/TFE, Moderate S/TFE, High S/TFE data sets were compared to No S/TFE control sets

2010-12-06 | E-GEOD-25690 | biostudies-arrayexpress

Global analysis of miRNA expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE

2010-12-06 | E-GEOD-25691 | biostudies-arrayexpress

FLAG-PHF3 interactome in HEK293 cells

Project description:FLAG-hPHF3 was transiently expressed in human HEK293 cells, followed by anti-FLAG immunoprecipitation, on-bead digest and NanoLC-MS analysis.

2022-02-17 | PXD026292 | Pride

Global analysis of miRNA expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE

2010-12-06 | GSE25691 | GEO

Global analysis of mRNA expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE

2010-12-06 | GSE25690 | GEO

Expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE

Project description:This SuperSeries is composed of the following subset Series: GSE25690: Global analysis of mRNA expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE. GSE25691: Global analysis of miRNA expression in prospectively purified human prostate orthotopic xenograft tumor cells with varying S/TFE. Refer to individual Series

2010-12-06 | E-GEOD-25692 | biostudies-arrayexpress

RNA-Seq Samples of siTFE3 in 8988T PDA Cell Line to Investigate Transcriptional Control of the Autophagy-Lysosome System

Project description:The activation of cellular quality control pathways to maintain metabolic homeostasis and mitigate diverse cellular stresses is emerging as a critical growth and survival mechanism in many cancers. Autophagy, a highly conserved cellular self-degradative process, is a key player in the initiation and maintenance of pancreatic ductal adenocarcinoma (PDA). However, the regulatory circuits that activate autophagy, and how they enable reprogramming of PDA cell metabolism are unknown. We now show that autophagy regulation in PDA occurs as part of a broader program that coordinates activation of lysosome biogenesis, function and nutrient scavenging, through constitutive activation of the MiT/TFE family of bHLH transcription factors. In PDA cells, the MiT/TFE proteins - MITF, TFE3 and TFEB - override a regulatory mechanism that controls their nuclear translocation, resulting in their constitutive activation. By orchestrating the expression of a coherent network of genes that induce high levels of lysosomal catabolic function, the MiT/TFE factors are required for proliferation and tumorigenicity of PDA cells. Importantly, unbiased global metabolite profiling reveals that MiT/TFE-dependent autophagy-lysosomal activation is specifically required to maintain intracellular AA pools in PDA. This AA flux is part of a program that is essential for metabolic homeostasis and bioenergetics of PDA but not for their non-transformed counterparts. These results identify the MiT/TFE transcription factors as master regulators of the autophagy-lysosomal system in PDA and demonstrate a central role of the autophagosome-lysosome compartment in maintaining tumor cell metabolism through alternative amino acid acquisition and utilization. Examination of mRNA levels in pancreatic ductal adenocarcinoma (PDA) cell line 8988T after treatment with siRNA for control or TFE3

2015-04-03 | E-GEOD-62077 | biostudies-arrayexpress

Expression data of Tfe3/Tfeb- or GFP-knocked-down RAW264 macrophages treated with or without iron

Project description:In an attempt to elucidate the role of MiT/TFE families in the iron-mediated phenotypic changes of macrophages, we performed DNA microarray analysis using ferric chloride-stimulated RAW264 cells transfected with Tfe3/Tfeb or GFP. A number of genes upregulated by ferric chloride treatment in siGFP-transfected RAW264 cells were decreased in siTfe3/Tfeb-transfected cells, suggesting MiT/TFE families are involved in phenotypic changes of macrophages induced by iron.

2021-01-27 | GSE157472 | GEO

Quantitative comparison of deparaffinisation, rehydration and extraction methods for FFPE tissue proteomics and phosphoproteomics

Project description:Formalin-fixed paraffin-embedded tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The sample preparation method chosen influences the number, intensity, and reproducibility of identifications. By comparing the performance of four deparaffinisation and rehydration methods, we found that heptane and methanol quantified the most protein groups whilst the most widely used xylene and ethanol quantified the least. We then modified five extraction methods from the literature based on their diverse lysis and digestion conditions before evaluating their performance using rat organs of the kidney, leg muscle, lung, and testis. All methods performed well except for SP3, that struggled with tissue lysis. Heat n’ Beat was the fastest, had the highest digestion efficiency, quantified protein groups, and lowest coefficient of variation across replicates. Strap produced the highest peptide yield and SPEED produced a ultraviolet quantitation interference. TFE produced the highest phosphoprecursor intensity with a 10-15% higher enrichment efficiency. We demonstrate that the choice of extraction method has a larger impact on the phosphoproteome than the proteome. We conclude by providing recommendations for choosing the most appropriate method for different settings.

2024-08-06 | PXD049062 | Pride

Seq-Well: A portable, low-cost platform for single-cell RNA-seq of low-input samples

Project description:Single-cell RNA -seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively parallel single-cell RNA -seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We characterize Seq-Well extensively and use it to profile thousands of primary human macrophages exposed to tuberculosis.

2017-02-17 | GSE92495 | GEO