Dataset Information

Defining the cellular proteolytic landscape with different controls

ABSTRACT: Mass spectrometry analysis of cellular targets of protein degradation

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Assaf Kacen

LAB HEAD: Yifat Merbl

PROVIDER: PXD009508 | Pride | 2018-10-11

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	HF1_7181_YMER_1511_1_010418.raw	Raw
	HF1_7181_YMER_1512_1_010418.raw	Raw
	HF1_7181_YMER_1513_1_010418.raw	Raw
	HF1_7181_YMER_1514_1_010418.raw	Raw
	HF1_7181_YMER_1515_1_010418.raw	Raw

Items per page:

1 - 5 of 19

Publications

Revealing the cellular degradome by mass spectrometry analysis of proteasome-cleaved peptides.

Wolf-Levy Hila H Javitt Aaron A Eisenberg-Lerner Avital A Kacen Assaf A Ulman Adi A Sheban Daoud D Dassa Bareket B Fishbain-Yoskovitz Vered V Carmona-Rivera Carmelo C Kramer Matthias P MP Nudel Neta N Regev Ifat I Zahavi Liron L Elinger Dalia D Kaplan Mariana J MJ Morgenstern David D Levin Yishai Y Merbl Yifat Y

Nature biotechnology 20181022

Cellular function is critically regulated through degradation of substrates by the proteasome. To enable direct analysis of naturally cleaved proteasomal peptides under physiological conditions, we developed mass spectrometry analysis of proteolytic peptides (MAPP), a method for proteasomal footprinting that allows for capture, isolation and analysis of proteasome-cleaved peptides. Application of MAPP to cancer cell lines as well as primary immune cells revealed dynamic modulation of the cellula ...[more]

PMID: 30346940

Similar Datasets

Project description:Motility and the coordination of moving food through the gastrointestinal tract rely on a complex network of neurons known as the enteric nervous system (ENS). Despite its critical function, many of the molecular mechanisms that direct the development of the ENS and the elaboration of neural network connections remain unknown. The goal of this study was to transcriptionally identify molecular pathways and candidate genes that drive specification, differentiation and the neural circuitry of specific neural progenitors, the phox2b expressing ENS cell lineage, during normal enteric nervous system development. Because ENS development is tightly linked to its environment, the transcriptional landscape of the cellular environment of the intestine was also analyzed.Thousands of zebrafish intestines were manually dissected from a transgenic line expressing green fluorescent protein under the phox2b regulatory elements [Tg(phox2b:EGFP) w37 ]. Fluorescence-activated cell sorting was used to separate GFP-positive phox2b expressing ENS progenitor and derivatives from GFP-negative intestinal cells. RNA-seq was performed to obtain accurate, reproducible transcriptional profiles and the unbiased detection of low level transcripts. Analysis revealed genes and pathways that may function in ENS cell determination, genes that may be identifiers of different ENS subtypes, and genes that define the non-neural cellular microenvironment of the ENS. Differential expression analysis between the two cell populations revealed the expected neuronal nature of the phox2b expressing lineage including the enrichment for genes required for neurogenesis and synaptogenesis, and identified many novel genes not previously associated with ENS development. Pathway analysis pointed to a high level of G-protein coupled pathway activation, and identified novel roles for candidate pathways such as the Nogo/Reticulon axon guidance pathway in ENS development.We report the comprehensive gene expression profiles of a lineage-specific population of enteric progenitors, their derivatives, and their microenvironment during normal enteric nervous system development. Our results confirm previously implicated genes and pathways required for ENS development, and also identify scores of novel candidate genes and pathways. Thus, our dataset suggests various potential mechanisms that drive ENS development facilitating characterization and discovery of novel therapeutic strategies to improve gastrointestinal disorders.