Multi-omic sample preparation
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ABSTRACT:
PROVIDER: PRJEB75435 | ENA |
REPOSITORIES: ENA
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Project description:A single microfluidic device for multi-omics analysis sample preparation
| PRJEB75436 | ENA
Project description:Sample preparation is a crucial step in bottom-up proteomics. Analytical performances of bottom-up proteomics can be improved by the miniaturization of sample preparation steps. Many microfluidic devices are proposed in the field of proteomics. But many of them are not capable of handling complex sample and do not integrate the processing and digestion steps. We propose a ChipFilter Proteolysis (CFP) microfluidic device derived from the Filter Aided Sample Preparation FASP method for the miniaturization of protein processing and digestion steps in bottom-up proteomics. The microchip has two reaction chambers of 0.6 µL volume separated by a protein filtration membrane in regenerated cellulose. Cell lysis, protein concentration and rapid chemical and enzymatic treatment can be performed in our microfluidic device. Complex proteomic samples like yeast protein extract have already been analyzed with our microchip. Compared to the traditional FASP method, our microfluidic device offers a better proteome coverage with ten times less starting material and eight times quicker protocol.
2020-04-29 | PXD016742 | Pride
Project description:Sample preparation is a crucial step in bottom-up proteomics. Analytical performances of bottom-up proteomics can be improved by the miniaturization of sample preparation steps. Many microfluidic devices are proposed in the field of proteomics. But many of them are not capable of handling complex sample and do not integrate the processing and digestion steps. We propose a ChipFilter Proteolysis (CFP) microfluidic device derived from the Filter Aided Sample Preparation FASP method for the miniaturization of protein processing and digestion steps in bottom-up proteomics. The microchip has two reaction chambers of 0.6 µL volume separated by a protein filtration membrane in regenerated cellulose. Cell lysis, protein concentration and rapid chemical and enzymatic treatment can be performed in our microfluidic device. Complex proteomic samples like yeast protein extract have already been analyzed with our microchip. Compared to the traditional FASP method, our microfluidic device offers a better proteome coverage with ten times less starting material and eight times quicker protocol.
2020-04-29 | PXD018066 | Pride
Project description:Dataset related to manuscript pertaining to multi-omics sample preparation.
2022-04-12 | MSV000089241 | GNPS
Project description:Dataset related to manuscript pertaining to multi-omics sample preparation.
2022-04-12 | MSV000089241 | MassIVE
Project description:Here, we show that a ChipFilter microfluidic device coupled to LC-MS/MS can successfully be used for identification of microbial proteins. Using cultures of E. coli, B. subtilis and S. cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow higher number of proteins and peptides identification than standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amount of 16 of these species.
2024-05-24 | PXD039581 | Pride
Project description:Assessment of RNA-seq Sample Preparation Methodology
| PRJNA862603 | ENA
Project description:Assessment of RNA-seq Sample Preparation Methodology
| PRJNA862601 | ENA
Project description:Investigation in bacterial transcriptomics is widely used to investigate gene regulation, bacterial susceptibility to antibiotics, host-pathogen interactions, and pathogenesis. Transcriptomics is crucially dependent on suitable methods to isolate and detect bacterial RNA. Microfluidic approaches offer ways of creating integrated point-of-care systems, analysing a sample from preparation, RNA isolation through to detection. Critical for on-chip diagnostics to deliver on their promise is that mRNA expression is not altered through the use microfluidic sample processing. Here, we investigate the impact on the use of a microfluidic sample processing system based on hydrodynamic separation upon RNA expression of bacteria isolated from blood to prove its suitability for further microfluidic test development. A 10 array study using total RNA recovered from bacteria isolated using the microfluidic device and total RNA recovered from bacteria that were not separated using the device were compared. Arrays were performed in 5 biological replicates from each condition
2016-04-01 | E-GEOD-68064 | biostudies-arrayexpress
Project description:Immunoassays have been used for decades in clinical laboratories to quantify proteins in serum/plasma samples. However, different limitations hinder their use in some cases. Mass spectrometry (MS)-based proteomics analysis has recently appeared as a promising option to assess panels of protein biomarkers and provide protein profiles useful for health state monitoring. Nevertheless, translation of MS-based proteomics into the clinics is still hampered by the complexity, the substantial time and human workforce necessary for sample preparation. The processing of plasma matrix is especially tricky as it contains more than 3000 proteins spanning in an extreme dynamic range (10e10) of concentrations. To address this pre-analytical challenge, we have conceived a microfluidic device (PepS) to automate and accelerate blood sample preparation for bottom-up MS-based proteomic analysis. The microfluidic cartridge is operated through a dedicated compact instrument providing fully automated fluid processing and thermal control. In less than 2 hours, PepS device enables whole blood collection at the bedside, plasma separation and calibration, depletion of albumin, protein digestion with trypsin and stabilization of tryptic peptides on solid phase extraction sorbent. The performance of PepS device was assessed using discovery proteomics and targeted proteomics on a panel of three protein biomarkers routinely assayed in clinical laboratories. This innovative microfluidic device and associated instrumentation is expected to streamline and simplify clinical proteomic studies.
2021-01-04 | PXD019403 | Pride