Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A KRAS-responsive long non-coding RNA controls microRNA

ABSTRACT: RNA Antisense Purification and Mass Spectrometry (RAP-MS) was performed to explore the potential RNA binding proteins of lncRNA KIMAT1

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

DISEASE(S): Non-small Cell Lung Carcinoma

SUBMITTER: Dave Lee

LAB HEAD: Michela Garofalo

PROVIDER: PXD024388 | Pride | 2021-03-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	020817_LS_AP.raw	Raw
	020817_LS_AP.raw__F009812_.mzid.gz	Mzid
	020817_LS_AP.raw__F009812_.mzid_020817_LS_AP.raw__F009812_.MGF	Mzid
	020817_LS_HIF.raw	Raw
	020817_LS_HIF.raw__F009814_.mzid.gz	Mzid

Items per page:

1 - 5 of 36

Similar Datasets

Study on the genomic changes in ColIa2 Cre x RBP-Jkappa loxp/loxp mice

Project description:Skin tumor formed in the ColIa2 Cre x RBP-Jkappa loxp/loxp mice was analyzed for genomic changes by comparing with normal tissues from the same mice. Genomic DNA were isolated from each individual tumor and compared with the DNA extracted from the brain tissue in the same mouse.

2012-04-30 | E-GEOD-36464 | biostudies-arrayexpress

IP-MS:Protein precipitated by antisense (AS) DNA oligomers crossing the junction site of circNEIL3

Project description:To identify the circNEIL3 interacting protein, we performed RNA pull-down assays after transfecting into cells with biotin-labeled sense (S) or antisense (AS) DNA oligomers crossing the junction site of circNEIL3, and the pull-down proteins were subjected to SDS-PAGE and Coomassie blue staining. ~45 kDa Band pulled down by the AS probe was specifically excised , digested and used for mass spectrometry analysis.

2023-10-24 | PXD039394 | Pride

The spliceosome factor USP39 promotes hepatocellular carcinoma malignancy through regulating mRNA splicing

Project description:Abnormal alternative splicing (AS) caused by alterations to splicing factors contributes to tumor progression. Nonetheless, the relevant targets and mechanisms remain elusive in hepatocellular carcinoma (HCC). Here, we reported that overexpression of Ubiquitin-specific protease 39 (USP39), a spliceosome component of the U4/U6.U5 tri-snRNP complex, is associated with poor clinical outcomes and proliferative signaling. Functionally, hepatocyte-specific USP39 knockin mice exhibited enhanced hepatocarcinogenesis. In vitro, USP39 promoted HCC cell proliferation and cell cycle progression in a spliceosome-dependent manner. Transcriptomic analysis revealed that USP39 depletion led to comprehensively impaired constitutive splicing and intriguingly, selective AS of hundreds of genes. USP39-mediated splicing switch of KANK2-S to KANK2-L increased the tumorigenic potential of HCC cells through accelerating KANK2 translation. Mechanistically, USP39 modulates exon inclusion/exclusion via interaction with SRSF6 or hnRNPC in a position-dependent manner. These findings highlight a role for USP39 as a splicing regulator in HCC biology and establishing its position-dependent splicing model.

2023-10-24 | PXD035928 | Pride

SerpinB2/TPPII regulates senescence

Project description:Tripeptidyl peptidase II (TPPII) degrades N-terminal tripeptides from proteins and peptides. Studies in both human and mice have shown that TPPII deficiency is linked to cellular immune-senescence, lifespan regulation, and the aging process. However, the mechanism of how TPPII participates in these processes is less clear. In this study, we established a chemical probe-based assay and found that while the mRNA and protein levels of TPPII were not altered during senescence, its enzymatic activity was reduced in senescent human fibroblasts. We also showed that elevation of serine protease inhibitor serpinB2 reduced TPPII activity in senescent cells. Moreover, suppression of TPPII led to elevation of lysosomal contents as well as TPPI and -galactosidase activities, suggesting that the lysosome biogenesis is induced to compensate for the reduction of TPPII activity in senescent cells. Together this study discloses a critical role of the serpinB2/TPPII signaling pathway in proteostasis during senescence. Since serpinB2 level can be increased by a variety of cellular stresses, reduction of TPPII activity through activation of serpinB2 might represent a common pathway for cells to respond to different stress conditions.

2022-05-31 | PXD033808 | Pride

Identification of human gene LOC107984012 interacting proteins in AC16 cardiomyocytes by pull-down assays coupled to MS

Project description:In this study, pull down assays combined with mass spectrometry analysis were performed in AC16 cardiomyocytes transfected with control plasmid (OE-Vector) or LOC107984012-overexpression plasmid to identify the repertoire of LOC107984012 interacting proteins. Pierce™ Magnetic RNA-Protein Pull-Down Kit (Thermo Fisher) provides reagents to efficiently enrich RNA Binding Proteins. Sense or antisense of LOC107984012 were in vitro transcription using the T7 RNA transcription system (Large Scale RNA ProductionSystem-T7, Promega) and biotin-labeled with the Pierce™ RNA 3’ End Desthiobiotinylation Kit (Thermo Scientific). RNA was then purified with QIAquick PCR Purification Kit (Qiagen). 30 μg of whole-cell protein lysates were incubated with purified biotinylated transcripts for 1 h at 4°C with rotation, then they were eluted for mass spectrometry identification.

2024-01-26 | PXD037001 | Pride

Dataset 2: Targets of SCoR-mediated Denitrosylation

Project description:Identification of targets of SNO-CoA- and SCoR-mediated denitrosylation in HEK293 cells expressing inducible nitric oxide synthase.

2018-12-11 | PXD011881 | Pride

Dataset 1: SNO-CoA Targets in Mouse Kidney

Project description:Identification of murine targets of SNO-CoA-mediated S-nitrosylation following treatment of mouse kidney lysate with SNO-CoA in combination with recombinant WT or K127A mutant SNO-CoA reductase.

2018-12-11 | PXD011880 | Pride

Identification of mouse lncRNA ENSMUST00000219456(GM32255) interacting proteins in HL-1 cardiomyocytes by pull-down assays coupled to MS

Project description:In this study, pull down assays combined with mass spectrometry analysis were performed in HL-1 cardiomyocytes transfected with control plasmid (OE-Vector) or LOC107984012-overexpression plasmid to identify the repertoire of LOC107984012 interacting proteins.

2024-01-26 | PXD036966 | Pride

An in-depth Mass Spectrometry Characterization of the SDS-PAGE Protein Profile of Legumins and Vicilins from Chickpea Seed

Project description:Chickpea (Cicer arietinum L.) seed proteins show a lot of functional properties leading this leg-ume an interesting component for the development of protein-enriched foods. However, both in-depth proteomic investigation and structural characterization of chickpea proteins seed are still lacking. In this paper we report a detailed characterization of chickpea seed protein fraction by means SDS-PAGE, in-gel protein digestion, high-resolution mass spectrometry, and database searching. By this approach twenty SDS gel bands were cut and analysed. While the majority of bands and the identified peptides were related to vicilin and legumin storage proteins, also metabolic functional proteins were detected. Legumins, as expected, were revealed at 45÷65 kDa, as whole subunits with the α- and β-chains linked together by a disulphide bond, but also at lower mass ranges (α- and β-chains migrating alone). Similarly, but not expected, also the vi-cilins were spread along the mass region between 65 and 23 kDa, with some of them identified in several bands. In-depth MS structural characterization allowed to determine that, although chickpea vicilins were always described as proteins lacking of cysteine residues, they contain this amino acid residue. Moreover, similarly to legumins, these storage proteins are firstly syn-thesized as pre-propolypeptides (Mr 50÷80 kDa), that may undergo to proteolytic steps that cut not only the signal peptides but also produce different subunits having lower molecular masses. Overall, about 360 different proteins specific of the Cicer arietinum L. species were identified and characterized, a result that up to date represents the most detailed description of seed’s proteome of this legume.

2024-06-23 | PXD049382 | Pride

Synthesis of flavonol-bearing probes and chemical proteomic analysis of Asteraceae petals in search of flavonoid enzymes

Project description:In flowers of Asteraceae, yellow flavonols bearing an additional hydroxyl group at positions 6 or 8 (ring A) contribute to petal UV-absorbing pigmentation patterns, which play a crucial role in attracting pollinating insects. Understanding the biogenesis of these special flavonols requires the identification of any specific enzyme involved in these incorporations of extra hydroxyl groups on the quercetin ring A. To this aim, flavonol-bearing biotinylated probes have been designed and synthesized to explore their ability to selectively capture target proteins or biosynthetic enzymes under oxidative activation. These probes demonstrate the ability to capture several flavonoid enzymes from Rudbeckia and Tagetes microsomes and allow the identification of uncharacterized candidates for novel flavonoid enzymes.

2023-07-20 | PXD041520 | 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