Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

O-GlcNAc Containing Proteins in Normal and Idiopathic Pulmonary Fibrosis Human Fibroblasts

ABSTRACT: Isolated normal and IPF fibroblasts were homogenized in cold MilliQ water using a bullet blender. Samples were centrifuged and inhibitors were added: HALT (Thermo Fisher Scientific), Z-Pugnac (Tocris), Thiamet G (Cayman Chemicals), and benzonase (E1014, Millipore, Sigma). O-GlcNAc enzymatic labeling and protein capturing was performed as described using a Click-IT enrichment kit following the manufacturer's protocol (cat no: C33368, C33372, and C10416; Thermo Fisher Scientific). Following an alkyne agarose bead enrichment, proteins were reduced (5 mM DTT, 30 min at 37 C), alkylated (40 mM iodoacetamide, 1 h at 37C) and digested with trypsin (1:50 enzyme/protein ratio). 0.5 ug of samples were analyzed by LC-MS/MS on a Q-Exactive HF-X mass spectrometer. Data was searched using MSFragger in match between runs mode.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Jennifer E. Kyle

PROVIDER: MSV000093453 | MassIVE | Tue Nov 21 15:52:00 GMT 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Urinary exosome microRNA signatures as a non-invasive prognostic biomarker for prostate cancer

Project description:We aimed to identify urinary exosomal miRNAs associated with PCa metastasis and develop a non-invasive risk-scoring model for PCa metastasis in this study. MiRNA profiles were examined using the Taqman low-density miRNA array (TLDA). Megaplex reverse transcription reactions and pre-amplification reactions were performed to increase the quantity of cDNA for miRNA expression analysis using the Megaplex PreAmp Primers Human Pool A and TaqMan PreAmp Master Mix (Thermo Fisher Scientific). MiRNA expression was evaluated via the TLDA panel A v2.0 (Thermo Fisher Scientific). Raw data were processed using the QuantStudio Real-Time PCR Software (Thermo Fisher Scientific) to determine a cycle threshold (Ct) value for each miRNA.

2021-06-07 | GSE173094 | GEO

Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcomas (CNV)

Project description:Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcoma

2019-08-23 | GSE119042 | GEO

Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcomas (expression)

Project description:Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcoma

2019-08-23 | GSE119041 | GEO

CIRCULATING SERUM MICRO-RNA AS NON-INVASIVE DIAGNOSTIC BIOMARKERS OF ENDOMETRIOSIS

Project description:Total RNA was extracted from 400 ul of serum with the miRNeasy Serum/Plasma advanced Kit (Qiagen) and quantified using the Qubit microRNA assay kit (Thermo Fisher Scientific). cDNA templates were prepared using the TaqMan Advanced miRNA cDNA Synthesis Kit (Thermo Fisher Scientific), starting from 10 ng of RNA. RT-qPCR carried out on a QuantStudio 12K Flex (Applied Biosystems) using the TaqMan OpenArray miRNA panel.

2024-10-30 | GSE279435 | GEO

Elucidating the Role of the Desmosome Protein p53 Apoptosis Effector Related to PMP-22 in Growth Hormone Tumors

Project description:An Affymetrix Human Gene 1.1 ST array plate (Thermo Fisher Scientific) was hybridized with 2.3 µg of fragmented and labeled single-stranded complementary DNA (cDNA)

2022-09-29 | GSE214226 | GEO

Hepatitis C virus induces HuR relocalization by coordinating PKC-δ and AMPK-α function

Project description:Huh7.5 cells were transfected with HCV-JFH1 RNAand harvested after 48h of transfection. Total proteins were extracted in IP lysis buffer (Pierce, Thermo Scientific) containing 1× halt-protease and phosphatase inhibitor cocktail (Thermo Fisher Scientific, USA) with intermediate vortexing followed by mild sonication. The lysate was centrifuged at 14,000 × g for 30 min at 4 °C. The supernatant was quantified by the BCA method (Thermo Fisher Scientific, USA). An equivalent amount (4 mg) of proteins from each condition was incubated with 3g of anti-HuR antibody for overnight at 4 °C. The immunocomplex was captured by using protein G Sepharose 4 fast flow beads (17-0618-01/ GE Healthcare). The immunoprecipitated complex was washed two times with IP lysis buffer and one time with mili-Q. Bound protein complexes were eluted in 50 µl SDS-PAGE 2X Laemmli sample buffer. The samples were resolved on 12% SDS–PAGE and stained with Coomassie stain (0.1% w/v). The gel was subjected to further in-gel mass spectrometry analysis.

2023-09-16 | PXD035903 | Pride

The ER stress sensor IRE1 interacts with STIM1 to promote store-operated calcium entry, T cell activation, and muscular differentiation

Project description:A quantitative phosphoproteomic study was performed on mouse embryonic fibroblasts (MEF) knocked-out of IRE1 protein and re rexpressin it culturen in 25mM glucose media. The chosen experimental strategy was to perform phosphopeptide enrichment associated with multiplex protein identification and quantification by LC-MSMS on a high-resolution mass spectrometer using tandem mass tag (TMT9; Thermo Fisher Scientific) technology and High- Select Fe-NTA Phosphopeptide Enrichment Kit (Thermo Fisher Scientific).

2023-12-08 | PXD046579 | Pride

The regulons of an OmpR-like transcription factor in Pseudomonas syringae pv. Actinidiae

Project description:A ChIP-seq assay was performed to identify the regulons of an ompR-like transcription factor (gene name: 13375, GenBank: AYL80818.1) in Pseudomonas syringae pv. actinidiae. An 13375-overexpressing mutant G1-OE13375, which constitutively express C-terminally Myc-tagged ompR-like gene in the 13375-deletion mutant G1Δ13375, was used in this study. The bacterial cells were cultured either in nutrition-rich KB medium or hrp-derepressing medium (HDM) at 25 C for 24 hours. A PierceTM Magnetic ChIP Kit (Cat. #: 26157, Thermo Fisher Scientific) and a ChIP-grade Myc-Tag Monoclonal Antibody (Myc.A7, Cat. #: MA121316, Thermo Fisher Scientific) were used for sample pretreatment and immunoprecipitation.

2022-12-13 | GSE220275 | GEO

Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcomas

Project description:Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcomas

| PRJNA487811 | ENA

Real-time quantitative PCR analysis of human low-density (LDNs) and normal-density neutrophils (NDNs)

Project description:NDNs and LDNs were isolated by density gradient centrifugation of PBMCs from 8 patients affected by tubercolosis (TB). In detail, RNA was extracted from NDNs and LDNs by Maxwell® RSC miRNA Tissue kit (Promega, Madison, USA), following manufacturer’s instructions. RNA concentration and quality was measured using NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific). Total RNA (600 ng) was reverse transcribed using the RT2 First Strand Kit (SABiosciences, Qiagen, UK). 84 human cytokines and chemokines were tested using the RT2 Profiler PCR Array Human Innate & Adaptive Immune Responses array (Qiagen). A semiquantitative real-time RT-PCR was performed using a real-time PCR detection system (QuantStudio 7 Flex Real-Time PCR System, Thermo Fisher Scientific) with a two-step thermal cycling: 95 °C for 10 min, followed by 40 cycles (95 °C for 15 sec, 60 °C for 1 min). Data were analysed using the RT² Profiler PCR Array Qiagen data analysis software, and ACTB and B2M as housekeeping genes.

2019-11-20 | GSE138948 | 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