PXD000304

PXD000304 is an original dataset announced via ProteomeXchange.

Title	DNMT DKO proteomic analyses
Description	This study aimed to investigate the link between DNA methylation and protein expression on a genome wide level, using a combination of MBD-sequencing and shotgun and positional proteomics on two human colon cancer cell lines: a wild type HCT116 cell line and a double knock out HCT116 cell line (DNMT1 -/- and DNMT3b -/-). The protein content of the HCT116 WT and DKO cell lines was not only analyzed using a standard shotgun proteomics approach, but also with the N-terminal COFRADIC technique (Staes et al., 2011), in order to determine the (alternative) translation start site of the expressed proteins.
HostingRepository	PRIDE
AnnounceDate	2015-10-02
AnnouncementXML	Submission_2015-10-02_05:11:05.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000304
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jolien Hollebeke
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	6x(13)C labeled L-lysine: 6.020129; S-carboxymethyl-L-cysteine: 58.005479; 6x(13)C: 4x(15)N labeled L-arginine; 2-pyrrolidone-5-carboxylic acid (Gln): -17.026549; 3x(2)H labeled N6-acetyl-L-lysine: 45.029395; 6x(13)C labeled L-arginine: 6.020129; L-methionine (S)-sulfoxide: 15.994915; N-acetylated residue: 42.010565
Instrument	instrument model: Orbitrap_Velos; LTQ Orbitrap Velos; instrument model: LTQ-Orbitrap(2011)

Revision	Datetime	Status	ChangeLog Entry
0	2013-06-27 02:43:12	ID requested
⏵ 1	2015-10-02 05:11:06	announced

Koch A, Gawron D, Steyaert S, Ndah E, Crapp, é J, De Keulenaer S, De Meester E, Ma M, Shen B, Gevaert K, Van Criekinge W, Van Damme P, Menschaert G, A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. Proteomics, 14(23-24):2688-98(2014) [pubmed]

submitter keyword: HCT116, DNMT1, DNMT3b, N-terminal COFRADIC, shotgun proteomics

Jolien Hollebeke
contact affiliation	VIB - Ghent University
contact email	jolien.hollebeke@vib-ugent.be
lab head
Jolien Hollebeke
contact affiliation	VIB - Ghent University
contact email	jolien.hollebeke@vib-ugent.be
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/2015/08/PXD000304

PRIDE project URI

• PRIDE
  1. PXD000304
     1. Label: PRIDE project
     2. Name: DNMT DKO proteomic analyses