Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A multi-omics dataset of human transcriptome and proteome stable reference

ABSTRACT: In recent years, the development of high-throughput omics technology has greatly promoted the development of biomedicine. However, the poor reproducibility of omics techniques limits its application. It is necessary to use standard reference materials of complex RNAs or proteins to test and calibrate the accuracy and reproducibility of omics workflows. Our study justified a omics standard reference material and reference datasets for transcriptomic and proteomics research. This helps to further standardize the workflow and data quality of omics techniques and thus promotes the application of omics technology in precision medicine.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Shaohua Lu

LAB HEAD: Gong Zhang

PROVIDER: PXD043389 | Pride | 2023-07-11

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1-9-DIA-SEARCH.sne	Other
	1-9DDA-proteinGroups.csv	Csv
	1-9DDA-proteinGroups_combined.rar	Other
	1-9proteinGroupsDIA.csv	Csv
	20200113_X3_2DDA1.raw	Raw

Items per page:

1 - 5 of 41

Similar Datasets

The SUMO protease SENP6 regulates the constitutive centromere-associated network by group

Project description:Project 1: Identification of SUMOylated proteins which are regulated by the SUMO protease SENP6. SENP6 knockdown was performed by two independent shRNAs and SUMOylated proteins were purified from U2OS expressing His10-tagged SUMO2 by means of Ni-NTA pulldown. Purified SUMOylated proteins were identified and quantified by label-free quantification. Project 2: Dynamics of chromatin-associated proteins influenced by SENP6. After siRNA-mediated knockdown of SENP6, chromatin fractions of U2OS cells were isolated and abundances of proteins were quantified. Project 3: Analysis of in vitro SUMOylated CENP-T for the presence of SUMOylated SUMO peptides. For this aim purified CENP-T-HA was in vitro SUMOylated with a SUMO Q87R mutant to reduce the length of the tryptic peptide and therefore to be able to identified sit-specific SUMOylation.

2019-09-13 | PXD011963 | Pride

Development of a Global Metabo-Lipid-Prote-omics Workflow to Compare Healthy Proximal and Distal Colonic Epithelium in Mice

Project description:A multimetabo-lipid-prote-omics workflow was developed to characterize the molecular interplay within proximal (PC) and distal (DC) colonic epithelium of healthy mice. This multiomics data set lays the foundation to better understand the two tissue types and can be used to study, for example, colon-related diseases like colorectal cancer or inflammatory bowel disease. First, the methyl tert-butyl ether extraction method was optimized, so that from a single tissue biopsy >350 reference-matched metabolites, >1850 reference-matched lipids, and >4500 proteins were detected by using targeted and untargeted metabolomics, untargeted lipidomics, and proteomics. Next, each omics-data set was analyzed individually and then merged with the additional omics disciplines to generate a deep understanding of the underlying complex regulatory network within the colon. Our data demonstrates, for example, differences in mucin formation, detected on substrate level as well as on enzyme level, and altered lipid metabolism by the detection of phospholipases hydrolyzing sphingomyelins to ceramides. In conclusion, the combination of the three mass spectrometry-based omics techniques can better entangle the functional and regional differences between PC and DC tissue compared to each single omics technique.

2024-09-04 | PXD046811 | Pride

RNA-Seq of Clostridium ljungdahlii with CO as the sources of carbon and energy in exponetial phase against stationary phase

Project description:More than 5 g/L ethanol was detected at 84 h in the late-exponential phase with 0.1 MPa at pH 6.0 in the batch fermentation of C. ljungdahlii grown autotrophically. Interestingly, ethanol started to be reassimilated in the stationary phase. In order to understand the metabolic flux of ethanol, comparative transcriptome between exponential and stationary phases were performed.

2022-07-26 | E-MTAB-7753 | biostudies-arrayexpress

RNA-Seq of Clostridium cellulovorans cultured in different carbon sources in exponential phase

Project description:When Clostridium cellulovorans cultured in different carbon sources respectively, with pH controlled at 7.0 in the fed-batch fermentation, the main product was butyrate. In order to understand the carbon and energy flux of Clostridium cellulovorans, comparative transcriptome in exponential phase was performed.

2022-11-21 | E-MTAB-12360 | biostudies-arrayexpress

Role of aldehyde dehydrogenase on the metabolic regulation in Clostridium ljungdahlii fermentation

Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. And C. ljungdahlii also grows in fructose fermentation. In theory, fructose is a more energetically favourable energy source than syngas in the fermentation of C. ljungdahlii. However, C. ljungdahlii grows insufficiently in fructose and produces less acetate and ethanol, compared to syngas fermentation. In this study, C. ljungdahlii wild type and mutants were fermented on fructose. C. ljungdahlii produced less ethanol than the ΔadhE1 mutant and consumed less fructose. The ΔadhE1+2 mutant cannot grow in the syngas fermentation and produced less ethanol among the three strains. The results showed that aldehyde dehydrogenase inactivation led to efficient metabolism in C. ljungdahlii and the bifunctional aldehyde/alcohol dehydrogenases inactivation led to decrease metabolism. Thus, comparative transcriptomes among cells grown on fructose of three strains were performed to investigate gene expression profiles based on three biological replicates.

2023-06-27 | E-MTAB-13020 | biostudies-arrayexpress

2 Role of aldehyde dehydrogenase on the metabolic regulation in Clostridium ljungdahlii fermentation

Project description:Clostridium ljungdahlii can utilize CO as energy source during autotrophic growth. C. ljungdahlii grows sufficiently in CO and produces ethanol as the main product. In this study, C. ljungdahlii wild type and mutant were fermented on CO. C. ljungdahlii produced more ethanol than the ΔadhE1 mutant. The results showed that aldehyde dehydrogenase inactivation led to inefficient metabolism in C. ljungdahlii. Thus, comparative transcriptomes among cells grown on CO of WT and ΔadhE1 mutant were performed to investigate gene expression profiles based on three biological replicates.

2023-06-27 | E-MTAB-13021 | biostudies-arrayexpress

Energy conservation and carbon flux arrangement in the fermentation of Clostridium ljungdahlii with CO or CO2/H2

Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. In theory, CO is a more energetically and thermodynamically favourable energy source than H2 in the gas fermentation of C. ljungdahlii. However, how C. ljungdahlii conserves energy for growth and ethanol/acetate formation grown on CO or CO2/H2 is not in great detail. In this study, C. ljungdahlii was fermented on CO and CO2/ H2 at pH 6.0 with 0.1 MPa gas pressure. C. ljungdahlii produced 27 g/L acetate, 9 g/L ethanol, 8 g/L 2,3-butanediol and traces of lactate in the presence of CO as energy source, while it produced 25.8  0.1 g/L acetate, 1.8  0.1 g/L ethanol, 0.7  0.01g/L 2,3-butanediol and trances of lactate in the same fermentation condition using H2 as energy source. Therefore, comparative transcriptomes between cells grown on CO and cells grown on H2/CO2 were performed to investigate gene expression profiles based on three biological replicates.

2020-04-01 | E-MTAB-8260 | biostudies-arrayexpress

Transcriptomic evaluation for human health risks in a drinking water plant

Project description:In this study, we intended to use trans-omics approach and some clinical examinations to systematically evaluate the human health risks of source of drinking water, effluent of conventional treatment and effluent of advanced treatment by quaternized magnetic microsphere in a drinking water plant.

2013-06-30 | E-MEXP-3766 | biostudies-arrayexpress

Enhanced solvent titer in the fermentation of Clostridium beijerinckii through application of metabolic controls

Project description:Clostridium beijerinckii is an anaerobic strain and well known for acetone-ethanol-butanol (ABE) fermentation using carbohydrates derived from cellulose or starch. During ABE fermentation, various byproducts are formed, mainly including acids (acetate, butyrate and lactate) and gas (hydrogen and carbon dioxide). recently, we found that Clostridium beijerinckii is able to produce a new product that had never been reported before and tightly regulated by pH and nitrogen source.

2021-12-02 | E-MTAB-11154 | biostudies-arrayexpress

Biomarkers discovery for Colorectal cancer

Project description:Identification of early diagnostic and prognostic biomarkers measurable in liquid biopsies remains a major challenge in oncology today. OMICs technologies cannot be applied on clinically precious human material as this is required in its integrity for routine pathology investigation. Hence all OMICs discovery today is done on residual and not clinically relevant material. In the study, we present a novel, non-destructive, procedure named EXPEL, which uses rapid, pressure-assisted, interstitial fluid extrusion, allowing for full clinical pathology and OMICs analysis (proteins, metabolites, miRNA and DNA) on the same specimen. To demonstrate this we engage in a simultaneous biomarker discovery and routine diagnostic analysis of human colorectal cancer and liver metastases. Biomarkers discovered with EXPEL methodology can be readily detected in human sera, allowing for unprecedented translation to the clinic. EXPEL method enables for the first time both clinicians and scientist to explore identical, fresh, clinical material regardless of origin and size.

2018-10-26 | PXD005693 | Pride