Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - NIH NGC Natural Products 2406 Standards analyzed by untargeted LC-MS/MS in negative ionization mode - part 1

ABSTRACT: NIH NGC Natural Products run by the Dorrestein Lab - 2406 Standards analyzed by untargeted LC-MS/MS in positive negative mode part 1. Note that each 96 well plate was divided as following: - One row represents a single plate. - Each well represents the pooling of the wells belonging to the same column for the corresponding plate. The MS/MS spectra have been uploaded on GNPS spectral library using an in-house script. Several adducts were retrieved for each compound. Some compounds could not be found during this process. Compound list can be found in Supplementary Files, as well as the LC-MS method used. Note that this dataset has been analyzed using one single LC method for both positive and negative ionization. Except few plates that were run with shorter LC-MS run in negative ion mode.

INSTRUMENT(S): Maxis II HD Bruker q-TOF

ORGANISM(S): Natural Products Isolated From Various Species

SUBMITTER: Ajit Jadhav Pieter Dorrestein

PROVIDER: MSV000080500 | GNPS | Tue Jan 24 13:19:00 GMT 2017

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Similar Datasets

GNPS - NIH NGC Natural Products 2406 Standards analyzed by untargeted LC-MS/MS in positive ionization mode - part 1

Project description:NIH NGC Natural Products run by the Dorrestein Lab - 2406 Standards analyzed by untargeted LC-MS/MS in positive ionization mode part 1. Note that each 96 well plate was divided as following: - One row represents a single plate. - Each well represents the pooling of the wells belonging to the same column for the corresponding plate. The MS/MS spectra have been uploaded on GNPS spectral library using an in-house script. Several adducts were retrieved for each compound. Some compounds could not be found during this process. Compound list can be found in Supplementary Files, as well as the LC-MS method used. Note that this dataset has been analyzed using one single LC method for both positive and negative ionization. Except few plates that were run with shorter LC-MS run in negative ion mode.

2017-01-23 | MSV000080492 | GNPS

GNPS - NIH NPAC ACONN Natural Products 2179 Standards analyzed by untargeted LC-MS/MS in negative ion mode part 2

Project description:NIH NPAC ACONN Natural Products 2179 Standards analyzed by untargeted LC-MS/MS in negative ion mode part 2. Note that each 96 well plate was divided as following: - One row represents a single plate. - Each well represents the pooling of the wells belonging to the same column for the corresponding plate. The MS/MS spectra have been uploaded on GNPS spectral library using an in-house script. Several adducts were retrieved for each compound. Some compounds could not be found during this process. Compound list can be found in Supplementary Files, as well as the LC-MS method used. Note that this dataset has been analyzed using one single LC method for both positive and negative ionization.

2017-02-18 | MSV000080555 | GNPS

GNPS - NIH NPAC ACONN Natural Products 2179 Standards analyzed by untargeted LC-MS/MS in positive ion mode part 2

Project description:NIH NPAC ACONN Natural Products 2179 Standards analyzed by untargeted LC-MS/MS in positive ion mode part 2. Note that each 96 well plate was divided as following: - One row represents a single plate. - Each well represents the pooling of the wells belonging to the same column for the corresponding plate. The MS/MS spectra have been uploaded on GNPS spectral library using an in-house script. Several adducts were retrieved for each compound. Some compounds could not be found during this process. Compound list can be found in Supplementary files, as well as the LC-MS method used. Note that this dataset has been analyzed using one single LC method for both positive and negative ionization.

2017-02-18 | MSV000080554 | GNPS

A Universal 384-Well Proteomic Sample Preparation Platform for High-Throughput Screening and Biomarker Discovery

Project description:Major advances have been made to develop an automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. An in-solution digest strategy is employed to generate peptides from the extracted proteins for LC-MS analysis in the 384-well plate. Method evaluation utilized HeLa cells cultured in the 384-well plate ranging from 500 – 10,000 cells. Digestion efficiency was excellent in comparison to the commercial digest peptides standard with minimal sample loss while improving sample preparation throughput by 20 – 40 fold. Analysis of six human cell types, which included two primary cell samples identified and quantified approximately 4,000 proteins for each sample in a single LC-MS/MS injection with as little as 100 – 10,000 cells depending on cell type demonstrating universality of the platform. Implementation of the comprehensive 384-well format protocol for processing cells to clean digested peptides enables large-scale biomarker validation and compound screening through proteomic analysis.

2021-06-14 | PXD019733 | Pride

Grouped ensemble coding of behavioral states by combinations of molecularly defined cell types

Project description:We used a plate-based method (SMART-SCRB) to transcriptionally profile manually picked single neurons from the paraventricular nucleus of hypothalamus (PVH) from 10 male Agrp-IRES-Cre crossed with Ai9 reporter mice, all >7 weeks old. For each mouse, the PVH was dissected and cells expressing the tdTomato reporter were manually selected and placed into wells of a series of 96-well plates. We used a plate-based method with cell and transcript barcording and reverse transcription in each well, followed by pooling and amplification using a modified SMART-Seq technology that yields digital 3' end counts of transcripts.

2020-06-30 | GSE148568 | GEO

Pseudo-temporal ordering of individual cells reveals regulators of differentiation

Project description:Single-cell expression profiling by RNA-Seq promises to exploit cell-to-cell variation in gene expression to reveal regulatory circuitry governing cell differentiation and other biological processes. Here, we describe Monocle, a novel unsupervised algorithm for ordering cells by progress through differentiation that dramatically increases temporal resolution of expression measurements. This reordering unmasks switch-like changes in expression of key regulatory factors, reveals sequentially organized waves of gene regulation, and exposes regulators of cell differentiation. A functional screen confirms that a number of these regulators dramatically alter the efficiency of myoblast differentiation, demonstrating that single-cell expression analysis with Monocle can uncover new regulators even in well-studied systems. We selected primary human myoblasts as a model system of cell differentiation to investigate whether ordering cells by progress revealed new regulators of the process. We sequenced RNA-Seq libraries from each of several hundred cells taken over a time-course of serum-induced differentiation. Please note that this dataset is a single-cell RNA-Seq data set, and each cell comes from a capture plate. Thus, each well of the plate was scored and flagged with several QC criteria prior to library construction, which are provided as sample characteristics; CONTROL indicates that this library is a off-chip tube control library constructed from RNA of approximately 250 cells and 'DEBRIS' indicates that the well contained visible debris (and may or may not include a cell). Libraries marked DEBRIS thus cannot be confirmed to come from a single cell.

2014-03-23 | E-GEOD-52529 | biostudies-arrayexpress

Cerebral Cavernous Malformation Plasma Samples

Project description:Plasma samples of patients diagnosed with CCM. Samples were run with a standard extraction (Plate 1 5x) and then again through a Phree Kit (Phree Kit Plate) to remove phospholipids. Data was acquired using a Bruker Maxis Impact and C18 RP-UHPLC using positive and negative polarity of LC-MS/MS.

2019-06-11 | MSV000083955 | MassIVE

Single cell RNA sequencing of primary-isolated erythroid progenitors [daughter cells]

Project description:Single cell mouse BFU-E (burst forming unit-erythroid ) were FACS-deposited into individual wells of a 96-well plate containing PCM either with or without 100 nM dexamethasone. After 16hrs cells from wells that contained a single pair of daughter cells were separated and each individual daughter cell transcriptome was obtained by single cell RNA-seq.

2019-03-01 | GSE117232 | GEO

A Universal 384-Well Proteomic Sample Preparation Platform for High-Throughput Screening and Biomarker Discovery

Project description:Major advances have been made to improve the sensitivity of mass analyzers, spectral quality, and the speed of data processing enabling more comprehensive proteome discovery and quantitation. While focus has recently begun shifting toward robust proteomic sample preparation efforts, a high throughput proteomics sample preparation is still lacking. We report the development of a highly-automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. Digestion efficiency was excellent in comparison to a commercial digest peptide standard with minimal sample loss while improving sample preparation throughput by 20- to 40-fold (<1 min/sample for entire process from cells to clean peptides). Analysis of six human cell types, which included two primary cell samples, identified and quantified approximately 4,000 proteins for each sample in a single HPLC-MS/MS injection with only 100 -10,000 cells, thus demonstrating universality of the platform.

2021-06-14 | PXD023374 | Pride

Single-cell RNA-seq of tailbuds from control, Pbx1/Pbx2 compound and Pbx1/Pbx2 double-knockout E8.5/E9.0 embryos.

Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). NMPs reside in the caudal lateral epiblast and tailbud, from where they sustain axial elongation. HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. To pinpoint the role of PBX proteins in the development of pre-somitic mesoderm, single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from the tailbuds of control, Pbx1/Pbx2 compound (Pbx1/2-com) and Pbx1/Pbx2 double-mutant (Pbx1/2-DKO) embryos at embryonic days 8.5 and 9.0. Single cells from at least three embryos per genotype and stage were FACS-sorted into 384-well capture plates, and scRNA-seq was performed using MARS-seq (Jaitin D.A. et al., Science, 343, 776-779 (2014)). As a spike-in internal control for batch-effect correction, 71 EpiSCs cultivated in vitro were sorted into each plate, together with 311 cells from embryonic tailbuds. Two wells were left empty in each plate, as a no-cell control during data analysis.

2021-07-21 | E-MTAB-9785 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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