Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SILAC-based quantitative proteomics analysis of lung cancer cells treated with a DNMTi drug decitabine

ABSTRACT: DNA methyltransferase inhibitors (DNMTi) has been shown to modulate pathways related to antigen processing/presentation, human leukocyte antigens (HLA), and interferon responses across different cancer types on the transcriptomic level (Li et al., 2014; Wrangle et al., 2013). Nevertheless, these transcriptomic changes may not fully reflect the alterations of surface proteins that provoke susceptibility to immunotherapy. Thus, we sought to obtain a comprehensive profile of surface proteins altered by decitabine (DAC) through isolating cell surface proteins from A549 human lung cancer cells before and after DAC treatment using EZ-link Sulfo-NHS-SS-Biotin-assisted biotinylation method, followed by SILAC-based quantitative proteomics approach.

INSTRUMENT(S): LTQ Orbitrap

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

SUBMITTER: Hsing-Chen Tsai

PROVIDER: MSV000084997 | MassIVE | Fri Feb 21 11:03:00 GMT 2020

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Frac-Seq Analysis of ZFC3H1 Knockdown U2OS Cells

Project description:We have found that depletion of the zinc finger protein ZFC3H1 inhibits the nuclear retention of these RNAs. ZFC3H1 forms a complex with MTR4 and PABPN1 (the PolyAdenylation EXosome Targeting complex (Meola et al 2016, Ogami et al 2017) and likely recruits the nuclear exosome for RNA degradation. Recently, we found that depletion of U1-70K, one protein component of the U1 snRNP spliceosomal complex, inhibits nuclear retention of 5’SS motif containing RNAs. The U1 snRNP complex recognizes and binds to the 5’SS motif and in vitro studies showed that U1-70K directly interact with a similar 5’SS motif through U1 snRNA binding (Gunderson et al 1999). Interestingly, we found that U1 snRNP is involved in targeting 5’SS motif containing mRNAs to nuclear speckles shortly following RNA transcription. In contrast, ZFC3H1 is involved in nuclear speckle localization post-transcriptionally and actively retain RNAs in these structures. Together, our results suggest a model where U1 snRNP interacts with the RNA via the 5’SS motif and targets mature mRNAs to nuclear speckles. Specifically, it suggests that misprocessed RNAs can be targeted to speckles (or other nucleoplasmic foci) and that these foci serve as a platform to recruit the nuclear exosome via ZFC3H1. Our results highlight a splicing independent role of U1 snRNP and how mRNA nuclear export function in nuclear surveillance to prevent the translation of aberrant proteins.

2022-03-31 | GSE176144 | GEO

SeaIce, Espegrend, Microscosm, Mnemi

Project description:454 dataset for Hosia, et al. Torstensson et al. Dinasquet et al.

| PRJEB7907 | ENA

Innate immune function of galectin-1 as a DAMP

Project description:Galectin-1 is a prototype member of the galectin family of b-galactoside-binding proteins with several immunoregulatory activities (Sundblad et al., 2017). Although this lectin exerts extracellular activities by cross-linking cell surface glycoconjugates, the mechanisms and molecular machinery involved in its secretion are uncertain as it lacks the classical signal sequence required for ER-Golgi release (Camby, 2006; Croci et al., 2014). To assess the global impact of galectin-1 on LPS-induced transcriptomic response, we performed RNAseq analysis of total RNAs from the spleen and the lungs of wild-type and Lgals1-/- mice injected with LPS.

2020-10-29 | GSE140892 | GEO

Expression (Gene) in the endothelial cells of the mouse female prefrontal cortex (PFC) following 10-day chronic social stress or 6-day subchronic variable stress exposure was compared to male [Male_SS_vs_Female_SS_or_SCVS]

Project description:Cell-specific transcriptomic analysis were performed on PFC endothelial cells of stress-susceptible (SS) and resilient (RES) mice along with females subjected to 6 days of subchronic variable stress to identify novel genes and pathways involved in stress responses. These gene lists were compared to published findings obtained in the male NAc following 10 days of chronic social stress exposure (Dudek et al., 2020)

2021-10-29 | GSE173797 | GEO

A Human Pluripotent Stem Cell Surface N-Glycoprotein resource including New Markers, Extracellular Epitopes, and Drug Targets

Project description:Detailed knowledge of cell surface proteins for isolating well-defined populations of human pluripotent stem cells (hPSCs) would significantly enhance their characterization and translational potential. Normal H9 human embryonic stem cells and the KB3 human induced pluripotent stem cell lines were analyzed by Cell Surface Capture Technology, and in parallel transcript profiles from five independent samples (i.e., Replicas 1-5 for each) were performed to facilitate protein and transcriptomic comparisons. The study compared gene expression profiles of pluripotent stem cells with Cell Surface Capture technology generated N-glycoprotein surfaceome analyses of the same cell types.

2014-03-12 | E-GEOD-55805 | biostudies-arrayexpress

Project description:Finn Et al.

| PRJNA433383 | ENA

Project description:Manavski et al

| PRJNA1192076 | ENA

A Human Pluripotent Stem Cell Surface N-Glycoprotein resource including New Markers, Extracellular Epitopes, and Drug Targets

2014-03-12 | GSE55805 | GEO

ST105-02: Deciphering and comparison of tumor mutational burden of MBT2 and LM8 mouse cancer cell lines

Project description:The aim of this project is to use high-throughput transcriptomic approach to decipher the tumor mutational burden (TMB) of two cancer cell lines, MBT2 (urothelial) and LM8 (osteosarcoma), syngeneic of the C3H/HeN mouse strain, and to compare them as biomarker of immunogenicity (Rizvi NA et al. Science, 2015, Sha D et al. Cancer Discovery, 2020).

2024-05-31 | GSE224642 | GEO

Discovery of the targets of the immune response to chronic myeloid leukemia in 3 patients using protein microarrays

Project description:Three patients who had relapsed chronic myeloid leukemia after allogeneic bone marrow transplant and received an immunotherapeutic intervention (donor lymphocyte infusion, or DLI) without further treatment were studied. The binding of serum immunoglobulins to proteins after immunotherapy was compared to before in two patients using Invitrogen ProtoArrays from a single lot. For a third patient, comparison was made between two timepoints after immunotherapy against one timepoint before using Invitrogen ProtoArrays from a separate lot. Significant interactions were determined by comparing each after sample separately against the before sample from that patient, using the Concentration-Dependent Analysis described in Marina et al., J Proteome Res, 2008. The goal was to identify proteins with significantly-increased reactivity after donor lymphocyte infusion. Keywords: Immune response discovery One sample from before and one sample from after immunotherapy were tested for 2 patients, and one sample from before and two samples from after immunotherapy were tested for a third patient.

2008-05-31 | E-GEOD-11565 | biostudies-arrayexpress

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