Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic response on ferroptosis induction via GPX4 KO in mouse embryonic fibroblasts

ABSTRACT: In the present study, we report proteome data of mouse embryonic fibroblasts (MEF cells) and immortalized mouse embryonic fibroblasts which are 4-OH-TAM-inducible Gpx4−/− (Pfa1 cells). Ferroptosis in Pfa1 cells was induced with Tamoxifen (Tam) addition and three timepoints were collected: 0h, 24h and 48h. Wild-type MEF cells were also measured as an alternative control without Tam addition. Raw data for HEK293 cells are provided as an independent quality control. MEF and Pfa1 cells (both kind gift from Marcus Conrad, Munich) were cultured in RPMI-1640 media (2 g/L glucose, 10% FBS, 2 mM Gibco GlutaMAX Supplement, 1% pen/strep) at 37C with 5% CO2 in a humidified incubator. Cells (300k) were seeded on Corning 100 mm tissue-culture treated culture dishes and incubated overnight. On the next day Pfa1 cells were treated with or without 1 µM Tam.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Embryonic Fibroblast, Cell Culture

SUBMITTER: Alexey Nesterenko

LAB HEAD: Vsevolod V. Belousov

PROVIDER: PXD040094 | Pride | 2023-04-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	210722CKP_FCMN302Hek2.mzML	Mzml
	210722CKP_FCMN302Hek2.mzid.gz	Mzid
	210722CKP_FCMN302Hek2.raw	Raw
	210722CKP_FCMN3_01.mzML	Mzml
	210722CKP_FCMN3_01.mzid.gz	Mzid

Items per page:

1 - 5 of 94

Similar Datasets

Proteomic shift in mouse embryonic fibroblasts Pfa1 during L-Buthionine-sulfoximine (BSO) induced ferroptosis

2023-04-12 | PXD041415 | Pride

Proteomic shift in mouse embryonic fibroblasts Pfa1 during ML210-induced ferroptosis

2023-07-10 | PXD041327 | Pride

Proteomic shift in mouse embryonic fibroblasts Pfa1 during erastin-induced ferroptosis

Project description:This report provides data on ferroptosis induced proteomic response in immortalized mouse embryonic fibroblasts which are 4-OH-TAM-inducible Gpx4−/− (referred to as Pfa1 cells). Pfa1 cells are a valuable, widespread and well characterized model for ferroptosis research. In the first part of this batch, we used Erastin to induce ferroptosis and collected samples at 0h, 24h and 48h after treatment. Untreated cells were used as a control. In the second part, we tested Liproxtatin-1 ferroptosis inhibitor on Tamoxifen-induced Pfa1 cells after 0h, 24h, 48h. Tamoxifen-induced ferroptosis activation of these cells are in PRIDE PXD040094. Pfa1 cells (a kind gift from Marcus Conrad, Munich) were cultured in RPMI-1640 media (2 g/L glucose, 10% FBS, 2 mM Gibco GlutaMAX Supplement, 1% pen/strep) at 37C with 5% CO2 in a humidified incubator. Cells (300k) were seeded on Corning 100 mm tissue-culture treated culture dishes and incubated overnight. On the next day Pfa1 cells were treated with or without 0.5 µM erastin (E7781, Sigma-Aldrich). For experiment on ferroptosis inhibition Pfa1 cells were treated with or without 1 µM Tamoxifen and 0.5 µM Liproxtatin-1 simultaneously.

2023-07-11 | PXD041463 | Pride

Determination of HOXA1 and HOXA9 target genes with inducible HOX constructs

Project description:Target genes of HOXA1 and HOXA9 were determined with the help of inducible HOX-ER constructs. For this purpose bone marrow was harvested from C57BL/6 mice and c-Kit positive progenitors were enriched by magnetic sorting (MACS technology, Miltenyi, Germany). After retroviral infection by spinoculation the cells were plated for three rounds in methylcellulose. Subsequently cells were maintained in liquid culture in RPMI1640 supplemented with murine recombinant cytokines at 100ng/ml (stem cell factor) and 10ng/ml (IL-3, IL-6, granulocyte/macrophage-colony stimulating factor) as well as 100nM 4-hydroxy-tamoxifen (TAM) for HOX activation.<br><br>For microarray analysis 4 independent cell lines were created for each HOX construct. RNA was isolated from cells in the presence of TAM and 72h after withdrawal of the inductor. Pairs of RNA replicates were pooled and two +TAM as well as two -TAM duplicates per HOX gene were hybridized to Agilent44K mouse expression arrays. Array processing and evaluation was done commercially according to Agilent specifications by ImaGenes (now SourceBioScience), Berlin, Germany.

2012-11-02 | E-MEXP-3648 | biostudies-arrayexpress

Tumor-Associated Macrophages Promote Colorectal Tumor Development Through Remodeling of Its Extracellular Matrix

Project description:Extracellular matrix (ECM) structural and compositional abnormalities are a hallmark of many cancers. Tumor associated macrophages (TAM) are considered pivotal players in mounting pro-tumoral functions; yet, their role in tumor-ECM remodeling remains largely ambiguous. Using an orthotopic murine model of colorectal cancer we defined two major CRC TAM subsets arising from Ly6Chi monocytes recruited in a CCR2-depedent manner. TAM-deficient CRC tumors established Ccr2-/- mice exhibited attenuated growth. Advanced imaging techniques revealed that the enhanced deposition, linearization and cross-linking of collagen fibers typical to tumor growth were absent in the Ccr2-/- tumors. Moreover, the Ccr2-/- tumors displayed altered ECM composition with 348 proteins that were differentially expressed in comparison with WT tumors, among them 46 were ECM related. Integrating transcriptomic and proteomic approaches we defined a TAM signature of ECM remodeling enzymes, structural and affiliated proteins. Specifically, were prominent proteins involved with the synthesis and assembly of collagen type I, IV and XIV. Finally, decellularized 3D ECM fragments extracted from WT tumors, but not from Ccr2-/- tumors or upstream healthy colon, enhanced tumor cell proliferation in vitro and tumor development in the native colonic environment. Collectively, our integrated biophysical-immunologic-omic approaches uncover new mechanistic insights of TAM-mediated remodeling of tumor ECM structure and composition.

2016-09-26 | PXD002094 | Pride

Illumina Sequencing data of Insulator Proteins and the co-factor dMes-4

Project description:The Drosophila insulator-binding proteins (IBPs) dCTCF/Beaf32 mark the physical borders of chromosomal domains involving co-factors that participate in long-range interactions. Chromosomal borders are further enriched in specific histone modifications yet the implication of histone modifiers and nucleosome dynamics remains largely unknown in such context. Here, we show that IBP depletion impairs nucleosome dynamics over genes flanked by their binding sites. Biochemical purification identifies a key histone methyltransferase of H3K36, NSD/dMes-4, as a novel co-factor of IBPs involved in chromatin accessibility, which specifically co-regulates hundreds of genes flanked by Beaf32/dCTCF. dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-mediated H3K36me3, RNA splicing and nucleosome positioning. Our results unveil a model for how IBPs regulate gene expression and nucleosome dynamics through NSD/dMes-4, which may contribute to regulate H3K27me3 spreading. Together, our data suggest a division of labor for how IBPs may dynamically regulate chromatin organization depending on distinct co-factors. ChIP-Seq profiles of H3K36 methylation and RNA Pol II in Drosophila S2 cell line (wild-type) cells

2014-04-30 | E-GEOD-57165 | biostudies-arrayexpress

Transcription profiling of mouse ES cells, neural precursor cells and embryonic fibroblasts

Project description:Expression profiles for isogenic (129SvJae x C57BL/6) murine embryonic stem (ES) cells, neural precursors (NPC) obtained through in vitro differentiation of the ES cells, and embryonic fibroblasts (MEF) obtained at day 13.5. Experiment Overall Design: 3 replicates of wt ES cells, 3 replicates of wt NPCs obtained by in vitro differentiation, 2 replicated of primary MEFs

2008-06-15 | E-GEOD-8024 | biostudies-arrayexpress

Endocytic and signalling function of stabilin-1 in tumor associated macrophages

Project description:Stabilin-1 is a scavenger/sorting receptor expressed by sinusoidal endothelial cells, alternatively-activated and tumor-associated macrophages (TAM) in several types of human cancer and mouse tumor models. We have found abundant expression of stabilin-1 on TAM in mouse model of mammary adenocarcinoma (TS/A) We performed microarrays with TAM isolated from wild type (wt) and stabilin-1 knock out (ko) mice in order to examine if stabilin-1 affects gene expression in TAM using mouse model of TS/A mammary adenocarcinoma Balb/c Wt and stabilin-1 ko female mice (8-12 weeks old) were inoculated s.c. with 5x10e6 TS/A cells. TAM were isolated from TS/A tumors 21 days after tumor challenge using CD11b MACS beads (Miltenyi Biotec), lysed for RNA and used for microarrays. Samples from 3 wt and 3 stabilin-1 ko mice were analyzed.

2014-10-30 | E-GEOD-55595 | biostudies-arrayexpress

ChIP-seq of the HOXA9 and MEIS1 transcription factors in SEM cells.

Project description:SEM cells were established from the peripheral blood of a 5-year-old girl in relapse with acute lymphoblastic leukaemia (ALL). SEM cells exhibit the t(4;11) chromosomal rearrangement, which leads to production of the MLL-AF4 fusion protein. Hematopoietic transcription factors including HOXA9 and MEIS1 are highly expressed in ALL. ChIP-seq was performed against HoxA9 and MEIS1 in SEM cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.

2012-05-31 | E-GEOD-38339 | biostudies-arrayexpress

MNASE_seq_of_AGO2_Knock_Down_HeLaS3_cells

Project description:We knocked down AGO2 protein by RNAi in HeLaS3 human cell line. The current experiment aims at comparing nucleosome positioning in control and AGO2 knock down cells. HeLaS3 cell were cultured in DMEM. Cells were transfected with AGO2 siRNAs (or control siRNA) at day 1. On day 4 MNAse digestion of chromatin was performed. Mnase-digested chromatin DNA fragments were sequenced by paired-end DNA-seq.

2015-05-17 | E-MTAB-1844 | 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