Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - MSMS-Chooser Methods - Q Exactive

ABSTRACT: The MSMS-Chooser workflow enables the rapid data acquisition and analysis of chemical standards and uploads the MSMS spectra to the community-driven mass spectrometry platform GNPS. Tune methods, instrument methods, and test data generated from the Q Exactive for the MSMS-Chooser workflow can be found here.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Not Applicable

SUBMITTER: Alan Jarmusch Pieter C Dorrestein

PROVIDER: MSV000084286 | GNPS |

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - MSMS-Chooser - GNPS00005

Project description:This is the fifth dataset for the new Chemical Standard to GNPS Library SOP workflow. MSMS-Chooser.

2019-10-21 | MSV000084479 | GNPS

GNPS - MSMS-Chooser - GNPS00004

Project description:This is the fourth dataset for the new Chemical Standard to GNPS Library SOP workflow MSMS-Chooser Uploaded and run by the Dorrestein Lab.

2019-10-23 | MSV000084493 | GNPS

GNPS - MSMS-Chooser - GNPS00003

Project description:This is the third dataset for the new Chemical Standard to GNPS Library SOP workflow MSMS-Chooser Uploaded and run by the Dorrestein Lab.

2019-10-23 | MSV000084492 | GNPS

GNPS - MSMS-Chooser - GNPS00006

Project description:This is the sixth dataset for the new Chemical Standard to GNPS Library SOP workflow MSMS-Chooser Uploaded and run by the Dorrestein Lab.

2019-10-23 | MSV000084495 | GNPS

GNPS - MSMS-Chooser - GNPS00007

Project description:This is the seventh dataset for the new Chemical Standard to GNPS Library SOP workflow MSMS-Chooser Uploaded and run by the Dorrestein Lab.

2019-10-23 | MSV000084496 | GNPS

GNPS - MSMS-Chooser - GNPS00002 CORRECT

Project description:This is the second dataset for the new Chemical Standard to GNPS Library SOP workflow MSMS-Chooser Uploaded and run by the Dorrestein Lab. These are the re-run samples from plate 2, after the instrument was fixed.

2019-10-23 | MSV000084494 | GNPS

The comparison of high-throughput single-cell RNA-seq methods

Project description:Here we compare the performance of these three approaches (inDrop, Drop-seq and 10x) using the same kind of sample with a unified data processing pipeline. We generated 2-3 replicates for each method using lymphoblastoid cell line GM12891. The average sequencing depth was around 50-60k reads per cell barcode. We also developed a versatile and rapid data processing workflow and applied it for all datasets. Cell capture efficiency, effective read ratio, barcode detection error and transcript detection sensitivity were analyzed as well.

2018-06-14 | GSE111912 | GEO

RNA Isolation Methods - Diverse Biofluids

Project description:RNA Isolation Methods - Diverse Biofluids

| PRJNA1013972 | ENA

Microbiome Methods Study

Project description:Advancing microbiome methods and bioinformatic approaches for biomarker discovery.

| PRJEB108443 | ENA

Systematic comparative analysis of strand-specific, cost-effective, RNA-seq library preparation methods for low input samples

Project description:Despite the precipitous decline in the cost of genome sequencing over the last few years, library preparation for RNA-seq is still laborious and expensive for high throughput screening for drug discovery. Limited availability of RNA generated by some experimental workflows poses an additional challenge and typically adds to the cost of RNA library preparation. In a search for low cost, automation-compatible RNA library preparation kits that also maintain strand specificity and are amenable to low input RNA quantities, we systematically tested two recent commercial technologies – Swift and Swift Rapid – using the Illumina TruSeq stranded mRNA, the de facto standard workflow for bulk transcriptomics, as our reference. We used the Universal Human Reference RNA (UHRR) (composed of equal quantities of total RNA from 10 human cancer cell lines) to benchmark differential gene expression in these kits, at input quantities ranging between 10 ng to 500 ng. Read quality and alignment metrics revealed high mapping efficiency and uniform read coverage through genes for all samples across all three kits. Normalized read counts between all treatment groups were in high agreement, with pairwise Pearson correlation coefficients >0.97. Compared to the Illumina TruSeq stranded mRNA kit, both Swift RNA library kits are cost effective and offer shorter workflow times enabled by their patented Adaptase technology. Furthermore, the Swift RNA kit allows for a relatively broader (and lower) input range, producing consistent results across diverse samples. The Swift Rapid RNA method is the fastest and most cost effective NGS workflow that is best suited for higher RNA yields, with the exact same RNA input range as the Illumina TruSeq kit. We also found the Swift RNA kit to produce the fewest number of differentially expressed genes and pathways attributable to input mRNA concentration.

2021-02-23 | GSE167300 | GEO

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