Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome Characterization of HFFs Upon NORAD lncRNA Knockdown

ABSTRACT: Mass spectrometry data were processed using MSFragger via FragPipe with default parameters. For downstream analysis, Perseus was used. The MaxLFQ intensity values were log2-transformed and filtered to include only proteins detected in at least two replicates. Missing values were imputed from a normal distribution. Statistical analysis was performed using a two-sample t-test, with a permutation-based FDR applied (S0 parameter = 0.1)

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hff-1 Cell

SUBMITTER: Amir Argoetti

LAB HEAD: Yael Mandel-Gutfreund

PROVIDER: PXD056160 | Pride | 2024-12-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	checksum.txt	Txt
	siCTRL1_Seq82994_480Ex2.pepXML	Pepxml
	siCTRL1_Seq82994_480Ex2.raw	Raw
	siCTRL2_Seq82995_480Ex2.pepXML	Pepxml
	siCTRL2_Seq82995_480Ex2.raw	Raw

Items per page:

1 - 5 of 13

Similar Datasets

STAT1 and STAT3 ChIP-seq for naive and effector memory (Tem) CD4 T-cells after IL-6 treatment

Project description:Naïve and activated T-cells has a different response to antigenic challenge. We examine whether a cytokine like IL-6 induces different responses through the Jak-STAT pathway to affect the functional characteristics of a given CD4 T‑cell subset. We isolated naïve and effector memory (Tem) CD4 T-cells to investigated STAT1 and STAT3 binding after 1-hour treatment with 20ng/ml IL-6 in the presence of anti-CD3/CD28.

2019-02-08 | E-MTAB-6273 | biostudies-arrayexpress

Opposing Roles of STAT1 and STAT3 in IL-21 Function in CD4+ T cells

Project description:Interleukin-21 (IL-21) is a type 1 cytokine essential for immune cell differentiation and function. Although IL-21 can activate several STAT family transcription factors, previous studies focused mainly on the role of STAT3 in IL-21 signaling. Here, we investigated the role of STAT1 and show that STAT1 and STAT3 have at least partially opposing roles in IL-21 signaling in CD4+ T cells. IL-21 induced STAT1 phosphorylation, and this was augmented in Stat3-deficient CD4+ T cells. RNA-Seq analysis of CD4+ T cells from Stat1- and Stat3-deficient mice revealed that both STAT1 and STAT3 are critical for IL-21-mediated gene regulation. Expression of some genes, including Tbx21 and Ifng, was differentially regulated by STAT1 and STAT3, and interestingly, ChIP-Seq analysis showed that STAT3 binding at Tbx21 and Ifng loci was attenuated in Stat1-deficient cells. Moreover, opposing actions of STAT1 and STAT3 on IFN- expression in CD4+ T cells were demonstrated in vivo during chronic lymphocytic choriomeningitis (LCMV) infection. Finally, IL-21-mediated induction of STAT1 phosphorylation, as well as IFNG and TBX21 expression, were higher in CD4+ T cells from patients with autosomal dominant hyper-IgE syndrome (AD-HIES), which is caused by STAT3 deficiency. These data indicate an interplay between STAT1 and STAT3 in fine-tuning IL-21 actions. Genome-wide transcription factors mapping and binding of STAT3 in mouse CD4+ T cells in both WT and Stat1-deficient mice. RNA-Seq is performed in mouse CD4+ T cells in WT, Stat1-deficient and Stat3-deficient mice.

2015-07-01 | E-GEOD-63204 | biostudies-arrayexpress

Cell signaling response to cytokines measured by high throughput microscopy

Project description:-

2017-09-19 | LDS-1125 | LINCS

High-throughput proteomics and phosphoproteomics of rat tissues using micro-flow Zeno SWATH

Project description:We investigated the combined sensitivity of micro-flow liquid chromatography with a ZenoTOF mass spectrometer for high throughput proteomic and phosphoproteomic analysis of rat tissues. Comparing the proteomes acquired using data-independent acquisition (DIA) on the ZenoTOF 7600 with the previous generation TripleTOF 6600, more proteins were quantified using a fifth of the sample load and a third of the instrument time. Zeno SWATH data was evaluated using replicate injections of rat organ digests to compare FragPipe and DIA-NN computational pipelines. FragPipe identified more proteins in 7 of the 8 rat organs, with an extra 12% and 17% observed in heart and muscle tissue respectively. The number of identified peptides per protein were higher with FragPipe and the precision of missing values across replicate injections was more consistent. Single-shot phosphopeptide enrichment from 100 µg rat tissue, without fractionation, was acquired using data-dependent acquisition (DDA) on both instruments. A total of 5,108 phosphosites were quantified with a negligible increase in phosphosites found using the ZenoTOF 7600 relative to the 6600. Using DIA on the ZenoTOF, 8,013 phosphosites were quantified using Spectronaut.

2024-06-02 | PXD045472 | Pride

ChIP seq: STAT1 and STAT3 transcription factors sense and interpret changes in inflammation through engagement of specific enhancers

Project description:Using ChIP-Seq analysis we explore regulation of gene expression changes during inflammatory peritonitis induced by challenge with bacterial ligands administered via the intra-peritoneal route. A resuspended lypholised supernatant of Staphylococcus epidermidis (SES) was administered with or without ex vivo generated CD4+ T-cells (Th1-polarised) to understand the role of adaptive immune responses in shaping inflammatory processes. To study the role of Signal transducer and Activator of Transcription 1 and 3 (STAT1/STAT3) we performed ChIP-seq on peritoneal membrane sections isolated from wt and Il-6 knockout mice three hours post-challenge. Membrane sections were snap frozen in liquid nitrogen prior to downstream processing using established ChIP-seq protocols (Illumina Truseq).

2022-04-04 | E-MTAB-10758 | biostudies-arrayexpress

Genome-wide binding signature of Signal transducer and activator of transcription (STAT) family in colorectal cancer HCT 116 cell

Project description:The excessive and continuous activated Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway leads to the proliferation and migration of malignant cells resulting in the occurrence and development of almost all of cancers. The defined gene sets specifically activated by different STAT proteins are relied on their genomic accessibility by the interplay of certain STAT proteins with other potential cofactors. However, we have no clue about the status of human activated STAT dimers in the nucleus, as well as the intercrossing modules of synergic, supplementary or competitive relationship among each other in colorectal cancer. In current study, chromatin immunoprecipitation sequencing (ChIP-seq) was conducted to explore the genome-scale binding signatures of STAT1, STAT2, STAT3, STAT5A/B and STAT6 in human HCT-116 CRC cells. Moreover, STAT3 binding on genomic DNA was also investigated in HCT116 cells with NR5A2 knockdown.

2021-11-08 | E-MTAB-11113 | biostudies-arrayexpress

Re-analysis of glycoproteomics data with MSFragger-Glyco

Project description:Reanalysis of submissions PXD011533 and PXD009476 using MSFragger-Glyco mode. Processed MSFragger results files (pepXML) and PSM tables (psm.tsv) supporting MSFragger-Glyco manuscript (Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Recent advances in methods for enrichment and mass spectrometric analysis of intact glycopeptides have produced large-scale glycoproteomics datasets, but interpreting this data remains challenging. We present MSFragger-Glyco, aa new glycoproteomics mode of the MSFragger search engine, called MSFragger-Glyco, for fast and sensitive identification of N- and O-linked glycopeptides and open glycan searches. Reanalysis of recent N-glycoproteomics data resulted in annotation of 80% more glycopeptide-spectrum matches (glycoPSMs) than previously reported. In published O-glycoproteomics data, our method more than doubled the number of glycoPSMs annotated when searching the same glycans as the original search and yielded 4-6-fold increases when expanding searches to include additional glycan compositions and other modifications. Expanded searches also revealed many sulfated and complex glycans that remained hidden to the original search.

2020-10-06 | PXD021196 | Pride

PCR-based microarray of tumor-infiltrating immune cells

Project description:Comparison of Stat3 downstream gene expression in tumor-infiltraing myeloid cells. cDNA from sample was added into the array plate containing primer of specific genes related to angiogensis and gene expression level was analyzed by real-time PCR. The array plate was purchased from SA Bioscience and catalog number is PAMM-024 (mouse angiogenesis PCR array)

2010-11-21 | E-MTAB-430 | biostudies-arrayexpress

DUSP2 dephosphorylates STAT3 at Y705 and S727 residues

Project description:In the related study, to determine whether DUSP2 definitively served as a phosphatase for STAT3, an in vitro phosphatase assay was used. Using S-tag beads, p-STAT3 was pulled down from IL-6 stimulated HEK293T cells transfected with STAT3-S-Tag. DUSP2 or control protein, which was purified from HEK293T cells transfected with DUSP2-FLAG or empty vector through extraction with anti-FLAG beads and elution with FLAG peptides, were incubated with p-STAT3-S-Tag-beads in phosphatase buffer. Then bound proteins were eluted and subjected to MS analysis. When compared with the control, incubation of STAT3 and DUSP2 led to dephosphorylation of two STAT3 residues that have been reported to promote its activity, namely tyrosine 705 and serine 727.

2015-10-13 | PXD002743 | Pride

in vitro kinase assays Identified of STAT1 phosphorylation sites-mediated LATS2

Project description:LATS1/2 are frequently down-regulated or mutated in endometrial cancer (EC), yet their exact role in endometrial tumor progression remains unclear. In this study, we unexpectedly discovered a new function of LATS1/2 in regulating MHC class I expression in EC. Knockout of LATS1/2 in EC cells led to significant down-regulation of multiple genes within the MHC/HLA Class I family, which weakened the killing effects of PBMCs on tumor cells. Importantly, we found that the regulation of MHC/HLA expression by LATS1/2 does not depend on the classical Hippo pathway but rather involves their direct interaction with STAT1. This interaction causes STAT1 to be phosphorylated at Ser727 or Ser532, promoting its accumulation and movement into the nucleus and enhancing the transcriptional activation of IRF1/NLRC5 on MHC-I. Additionally, we demonstrated that the kinase-dead mutant LATS1/2 weakens STAT1 phosphorylation at Ser727, supporting our findings. Our results show a positive correlation between the expression levels of LATS1/2, MHC-I, CD8, and p-STAT1 in tissue samples of EC, providing further evidence to support our discoveries. Overall, our findings reveal novel molecular mechanisms underlying tumor immunogenicity deficiency and suggest that LATS1/2 may serve as an immunotherapy biomarker for targeting EC.

2024-06-16 | PXD043500 | 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