Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Vendor raw files for leucine supplementation in STZ-induced T1DM mice

ABSTRACT: Vendor raw LC-MS/MS data and supporting files for the study "Leucine supplementation modulates lipid metabolism in STZ-induced type 1 diabetic mice". Waters Xevo G2-XS QTOF with ACQUITY BEH C18 column in positive ESI mode. Structured metadata, and the full LCMS protocol are included. Raw vendor files are provided as 16 multi-part 7z archives: RAW files.7z.001 ... RAW files.7z.016. Please see README_reassembly.txt for reassembly.

INSTRUMENT(S): Xevo G2-S QTof

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Jengyuan Yao

PROVIDER: MSV000099368 | MassIVE | Fri Oct 03 01:45:00 BST 2025

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Prospective Collection of PillCam SB3 Videos and Raw Data Files for Future Developments (SODA)

Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports

| 2291850 | ecrin-mdr-crc

Exome sequencing in classic Hairy cell leukaemia reveals widespread variation in acquired somatic mutations between individual tumours apart from the signature BRAF V(600)E lesion

Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.

2016-02-01 | E-MTAB-4313 | biostudies-arrayexpress

Differentially expression profiling in Hashimoto's thyroiditis (HT), papillary thyroid carcinoma (PTC) with HT in background, PTC without HT in background, micro PTC (mPTC), and three normal thyroid samples (TN).

Project description:Experiment: Establishment of expression profiles in HT, PTC with HT, PTC without HT, and mPTC in comparison to TN samples. TN samples were downloaded as CEL files from the repository of the microarray vendor. Biostatistical analysis focussed in first instance on identifying genes and biofunctions related to HT and PTC with HT.

2020-06-16 | GSE138198 | GEO

RNAseq analysis of treatment-resistant and sensitive breast cancer patient-derived organoids with paclitaxel treatments

Project description:Huntsman Cancer Institute (HCI)-001 patient-derived organoids (PDOs) and HCI-002 PDOs obtained from Huntsman Cancer Institute, University of Utah (Nat Med. 2011 Oct 23;17(11):1514-20). Purpose: The goals of this study is to identify molecular pathways and genes that are involved in the treatment responsiveness of breast cancer PDOs. Methods: mRNA profiles of HCI-001 and HCI-002 PDOs were generated by Illumina NovaSeq 6000 platform for paired-end sequencing, 150-bp read length, for about 20 million raw reads per sample. RNA sequencing FASTQ files were processed with HISAT2 aligner in default mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89). Differential gene expression analysis was performed using DESeq2 software. Enrichment analysis was performed using ClusterProfiler software. Results: We mapped about 20 million sequence reads per sample to the human genome (build HG38) in the RNAs of HCI-001 and HCI-002 PDOs treated with paclitaxel or vehicle. We used a minimum expression cut-off of 1 FPKM in order to exclude low-levels genes and the RNA-seq data confirmed the difference expression of 67 known apoptosis-regulatory genes in treatment-sensitive PDOs (HCI-002) compare to treatment-resistant PDOs (HCI-001). Conclusions: This study identified apoptosis-regulatory genes that are differentially induced or represeed in treatment-sensitive PDOs (HCI-002) or treatment-resistant PDOs (HCI-001).

2021-09-09 | GSE183477 | GEO

Immune effects of CMP-001 vs. controls on various immune cell subsets

Project description:Purpose: The goal of this study was to investigate the TLR9 specific immune effects of anti-Qbeta-coated CMP-001 using the following groups: untreated, anti-Qbeta coated CMP-001, anti-Qbeta coated CMP-001 with methylated and thus, inactive ODN (mCMP-001), and G10 (naked TLR9 agonist). Methods: Unfractionated PBMCs from a healthy donor were isolated via ficol gradient and treated with and without anti-Qbeta coated CMP-001 (10ug/ml), anti-Qbeta coated mCMP-001 (inactive ODN; 10ug/ml), or G10 (naked TLR9 agonist; 2.5ug/ml) for 24 hours. Untreated and treated fractions were sequenced on an Illumina NovaSeq 6000 system. FASTQ files were generated from basecall files with the bcl2fastq software (Illumina) provided by the University of Iowa Institute of Human Genetics. Data files were subsequently downloaded to Argon and mapped to the prebuilt GRCh38 genome with CellRanger (version 3.0.1). After initial mapping datasets were merged together and clustering was performed based on merged data sets using Cell Ranger software. Cells with unique gene counts fewer than 300 or more than 4,000 per cell were eliminated along with a mitochondria gene cutoff of 25%. Log normalization of aggregated reads was performed with Seurat (version 3.0.2) using a scale factor of 10,000. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1). Results: A total of 17,280 cells were recovered after filtering. Clusters were identified based on expression of unique gene markers. Differential expression analysis identified genes enriched in each populatin of cells corresponding to untreated versus treated libraries. Particular empasis was given to genes enriched in monocytes. Conclusions: We report that CMP-001 induces a variety of immune responses in each cell cluster, with a unique gene signature displayed by monocytes.

2021-06-30 | GSE172493 | GEO

The Neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory.

Project description:We performed an RNA Sequencing experiment on dorsal hippocampal tissue from four groups of animals: Baf53b+/- homecage (Baf53b+/- HC); Baf53b+/- behavior (Baf53b+/- Beh); wildtype homecage (WT HC); and wildtype behavior (WT Beh). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed thirty minutes following Object Location Memory training. The objective of this study was to examine activity regulated gene expression following a learning event (HC vs Beh) in wildtype and Baf53b+/- mutant mice.

2013-03-24 | GSE44229 | GEO

Aird: A computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time

Project description:We describe "Aird", an opensource and computation-oriented format with controllable precision, flexible indexing strategies, and high compression rate. Aird provides a novel compressor called Zlib-Diff-PforDelta (ZDPD) for m/z data. Compared with Zlib only, m/z data size is about 55% lower in Aird on average. With the high-speed decoding and encoding performance brought by the Single Instruction Multiple Data(SIMD) technology used in the ZDPD, Aird merely takes 33% decoding time compared with Zlib. We used the open dataset HYE, which contains 48 raw files from SCIEX TripleTOF 5600 and TripleTOF6600. The total file size is 206GB as the vendor format. The total size increases to 854GB after converting to mzML with 32-bit encoding precision. While it takes only 189GB when using Aird. Aird uses JavaScript Object Notation (JSON) for metadata storage. Aird-SDK is written in Java and AirdPro is a GUI client for vendor file converting which is written in C#. They are freely available at https://github.com/CSi-Studio/Aird-SDK and https://github.com/CSi-Studio/AirdPro.

2021-04-12 | PXD025142 | Pride

Proteomic dissection of CFAP44 deficient axonemes

Project description:Leishmania are protists (class: Kinetoplastida) with a single multifunctional flagellum, which forms a canonical motile 9+2 microtubule axoneme in the promastigote forms. Deletion of gene CFAP44 (LmxM.14.1430) caused a reduction in promastigote motility (Beneke et al., PLoS Pathogens, 2019; accepted). To study the changes in protein composition in CFAP44 deficient axonemes, flagellar skeletons were isolated from CFAP44 knockout mutants and the parental cell line L. mex Cas9 T7 (Beneke et al., R Soc Open Sci. 2017; 4(5):170095) using a modified version of the method by Robinson et al., (Methods Enzymol. 1991; 196:285-99). Liquid chromatography tandem mass spectrometry and a label-free quantitation method (SINQ; Trudgian et al., 2011, Proteomics 10.1002) were used to identify proteins enriched in each fraction. This PRIDE upload contains .RAW and .XML files, as well as the SINQ quantification output file “SINQ_raw_data”. XML files are named SUB9810; MSS11680. .RAW files are structured as follows: “CFAP44 mutants: Qex01_SVH_180422_TomBeneke_B29_F_001”; “Cas9 T7 parentals: Qex01_SVH_180422_TomBeneke_Cas9_F_005”.

2020-01-20 | PXD014077 | Pride

GNPS - Malpighiaceae plants (9 species)

Project description:Analyses of 9 Brazilian Malpighiaceae species (leaves). Dried plant material were extracted, with EtOH80%. Positive and Negative ionization mode analises. LC-MS/MS performed in an Waters Acquity UPLC H-Class (Waters) using a Acquity BEH Shield RP18 reverse phase UHPLC column (1.7 um, 100 x 2.1 mm) and Xevo G2-XS QToF Mass Spectrometer (Waters) equipped with ESI source.

2020-03-19 | MSV000085121 | GNPS

The Leishmania mexicana promastigote flagellar proteome

Project description:Leishmania are protists (class: Kinetoplastida) with a single multifunctional flagellum used for motility, attachment to the sand fly vector and sensory functions. To discover the protein composition of the L. mexicana promastigote flagellum, we fractionated L. mexicana promastigotes by mechanical shearing and differential centrifugation into four fractions: detergent soluble (Fs) and insoluble (Fi) fractions of isolated flagella and detergent soluble (Cs) and insoluble fractions (Ci) of deflagellated cell body remnants. A label-free quantitation method (SINQ; Trudgian et al., 2011, Proteomics 10.1002) was used to identify proteins enriched in each of the four fractions. This PRIDE upload contains .RAW, .MGF and .XML files, as well as the SINQ quantification output file “SINQ_raw_data” and the genome sequence annotation used for protein identification “MFiebig_20140619” (Fiebig et al., 2015, PLoS Pathogens II:e1005186). XML files are named SUB7467; MSS10859. .RAW and .MGF files are structured as follows (for each fraction there are eight files, corresponding to individual gel pieces): “Ci: C131121_030; C131121_031; C131121_032; C131121_033; C131121_034; C131121_035; C131121_036; C131121_037”, “Cs: C131121_040; C131121_041; C131121_042; C131121_043; C131121_044; C131121_045; C131121_046; C131121_047”, “Fi: C131121_010; C131121_011; C131121_012; C131121_013; C131121_014; C131121_015; C131121_016; C131121_017”, “Fs: C131121_020; C131121_021; C131121_022; C131121_023; C131121_024; C131121_025; C131121_026; C131121_027”.

2018-12-14 | PXD011057 | Pride

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