Browse
Submit Data
Databases
API
Help

Dataset Information

228 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LC-MS/MS of human T-ALL following 12h of ATR inhibition

ABSTRACT: Quantitative proteomic and phosphoproteomic analysis of the human T-ALL cell line, CCRF CEM, following 12 hours of ATR inhibiton using the Vertex drug, VE-822.

INSTRUMENT(S): LTQ Orbitrap, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell, Blood

DISEASE(S): Acute Leukemia

SUBMITTER: Joseph Capri

LAB HEAD: Caius Radu

PROVIDER: PXD006702 | Pride | 2017-07-31

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CEM_ATRi_phospho_evidence.txt	Txt
	CEM_ATRi_total-proteome_evidence.txt	Txt
	CEM_ATRi_total-proteome_proteinGroups.txt	Txt
	CEM_PD-release_evidence.txt	Txt
	CEM_PD-release_proteinGroups.txt	Txt

Items per page:

1 - 5 of 109

Similar Datasets

Dynamic changes in proteome and phosphoproteome following glutamate excitotoxicity in cultured primary cortical neurons

Project description:Excitotoxicity caused by over-stimulation of the ionotropic glutamate receptors is a key neuronal cell death process underpinning brain damage in acute and chronic neurological disorders such as ischaemic stroke, traumatic brain injury, and neurodegenerative diseases. Exactly how neurons die in excitotoxicity still remains unclear and is an important area of research in the field of neuroscience. In this current project we wanted to explore the global changes in proteome and phosphoproteome following glutamate excitotoxicity in cultured primary cortical neurons.

2019-03-07 | PXD008353 | Pride

Dynamic profiling of the protein life cycle in response to pathogens (protein)

Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress

Human CEM Cells: Control vs. 2h or 4.5h Cluvenone Treated

Project description:Transcriptional profiling of human CEM cells comparing control untreated CEM cells with either 2h or 4.5h cluvenone-treated CEM cells. Two-timepoint experiment, CEM vs. Cluvenone-Treated CEM (2h and 4.5h). Biological replicates: 4 control, 4 2h-treated, 4 4.5h-treated, independently grown and harvested. Pooled controls. One replicate per array.

2010-08-11 | E-GEOD-23536 | biostudies-arrayexpress

Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes

Project description:Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RNA polymerase II (Pol II), but are also affected by RNA turnover rate. Here, we demonstrate that integrated analysis of genome-wide TF occupancy, Pol II binding and steady-state RNA levels provide important insights in gene regulatory mechanisms. Pol II occupancy, as detected by Pol II ChIP-seq, was found to correlate better with TF occupancy compared to steady-state RNA levels and is thus a more precise readout for the primary transcriptional mechanisms that are triggered by signal transduction. Furthermore, analysis of differential Pol II occupancy and RNA-seq levels identified genes with high Pol II occupancy and relatively low RNA levels and vice versa. These categories are strongly enriched for genes from different functional classes. Our results demonstrate a complementary value in Pol II chip-seq and RNA-seq approaches for better understanding of gene expression regulation. 3 replicates of RNAPII ChIP-seq and RNA-seq under normal and Wnt suppressed conditions

2012-03-09 | E-GEOD-36349 | biostudies-arrayexpress

Region-specific proteome changes of the intestinal epithelium during aging and dietary restriction

Project description:The small intestine is responsible for nutrient absorption and it is one of the most important interfaces between the environment and our body. During aging, changes in the structure of the epithelium lead to food malabsorption and reduced barrier function thus increasing disease risk in aging. The molecular drivers of these alterations remain poorly understood. Here, we compared the proteomes of small intestinal crypts from mice across different anatomical regions and age groups. We found that aging alters epithelial immune responses, metabolic networks and stem cell proliferation, and it is accompanied by a region-dependent skewing in the cellular composition of the intestinal epithelium. Of note, a short period of dietary restriction followed by re-feeding partially restores the epithelium to a youthful state by promoting the differentiation of intestinal stem cells (ISCs) towards the secretory lineage. Using in vitro and in vivo studies, we identify Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2) – the rate limiting enzyme in the synthesis of ketone bodies – as a modulator of ISCs differentiation, which responds to dietary changes. This study provides an atlas of age-dependent proteome changes in defined regions of the intestinal epithelium and characterizes how young and old mice adapt to drastic changes of diet, such as dietary restriction and re-feeding.

2020-04-29 | PXD014311 | Pride

PAR-CLIP for JARID2 in mouse embryonic stem cells

Project description:This experiment was designed to identify RNAs making direct contact with JARID2 in mouse embryonic stem cells E14 cells were pulsed with 4-SU, irradiated with UV, and subjected to JARID2 immunoprecipitation.

2013-12-25 | E-GEOD-48517 | biostudies-arrayexpress

PAR-CLIP for JARID2 before and after differentiation of mouse embryonic stem cells

Project description:This experiment was designed to indentify RNAs making direct contact JARID2 as mouse ESCs differentiate E14 WT were left untreated or differentiated with 2 M-BM-5M RA for 24 hrs. In both cases, ceslls were pulsed with 4-SU, irradiated with UV, and subjected to JARID2 immunoprecipitation.

2014-08-20 | E-GEOD-60516 | biostudies-arrayexpress

PAR-CLIP for HA-tagged EZH2 in mouse embryonic stem cells

Project description:This experiment was designed to indentify RNAs making direct contact with EZH2 in mouse embryonic stem cells E14 with an integrated transgene encoding HA-EZH2 were pulsed with 4-SU, irradiated with UV, and subjected to HA immunoprecipitation.

2013-10-19 | E-GEOD-49433 | biostudies-arrayexpress

Genome-wide transcription start site determination of Geobacter sulfurreducens under multiple growth conditions

Project description:Determine the transcription start sites at 1-bp resolution across the entire G. sulfurreducens genome in multiple growth conditions, including fresh water acetate-fumarate (FWAF) medium, nitrogen limitation and growth on electrode. Special capture of the 5' end of primary transcripts in G. sulfurreducens and sequencing with Illumina Genome Analyzer II.

2010-07-01 | E-GEOD-22511 | biostudies-arrayexpress

Human Immunodeficiency Virus Tat Directly Interacts with a Specific Set of Cellular RNAs

Project description:We have used RNA immunoprecipitation to identify the set of mRNAs that HIV-1 Tat interacts with in T-cells. We have also performed measurements of relative RNA abundance to determine if Tat binding is associated with an increase in RNA abundance in Tat-expressing T-cells and during HIV infection of primary T-cells. We have also used RNA IP and ChIP-Chip to compare the RNAs with which Tat interacts with to the RNAs that RISC interacts with and the genes associated with pTEF-b.

2013-11-05 | E-MEXP-3199 | 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