PXD024689

PXD024689 is an original dataset announced via ProteomeXchange.

Title	Analysis of barley chromosomal proteome: a multiapproach exploration of flow cytometry-sorted mitotic chromosomes
Description	Proteins contribute to the structure of chromatin and regulate its functions. The basic building block of chromatin in eukaryotes is the nucleosome containing histones. Structural maintenance of chromosomes complexes perform the assembly of genomic DNA into the higher organizational structures of interphase chromatin as well as the compact arrangement of dividing chromosomes. Here, proteins were extracted from flow cytometry-sorted barley mitotic chromosomes after a nuclease treatment to remove DNA. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system prior to liquid chromatography coupled to tandem mass spectrometry. Nuclear and chromosomal proteins (almost 900 identifications) were then classified based on a combination of software prediction results, available database localization information, sequence homology, and domain representation. The degree of enrichment of the chromosome samples by chromosomal proteins was evaluated by comparing the results with controls (depleted flow cytometric fraction and initial cell lyzate). A biological context evaluation indicated the presence of several groups of abundant proteins including histone variants, topoisomerase 2, PARP2, Condensin complex subunits, and many proteins with chromatin-related functions. Interestingly, nucleolar proteins were found as wells as proteins documenting processes related to replication, transcription and DNA repair in barley mitotic chromosomes.
HostingRepository	PRIDE
AnnounceDate	2021-07-21
AnnouncementXML	Submission_2021-07-21_14:14:09.897.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ivo Chamrad
SpeciesList	scientific name: Hordeum vulgare (Barley); NCBI TaxID: 4513;
ModificationList	monohydroxylated residue; acetylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	maXis

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-11 23:10:23	ID requested
⏵ 1	2021-07-21 14:14:10	announced

Dataset with its publication pending

submitter keyword: barley, chromatin, chromosome, prediction, flow cytometry, mass spectrometry, proteomics

Marek Sebela
contact affiliation	Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, Olomouc, Czech Republic
contact email	marek.sebela@upol.cz
lab head
Ivo Chamrad
contact affiliation	Palacky University, Olomouc
contact email	ivo.chamrad@upol.cz
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD024689

PRIDE project URI

• PRIDE
  1. PXD024689
     1. Label: PRIDE project
     2. Name: Analysis of barley chromosomal proteome: a multiapproach exploration of flow cytometry-sorted mitotic chromosomes