PXD005703

PXD005703 is an original dataset announced via ProteomeXchange.

Title	Time-course proteomics analysis of human regulatory T cell (Treg) differentiation
Description	Human naïve CD4+ T cells (CD4+ CD45RA+ CD25- CD45RO- CD8- CD14- CD15- CD16- CD19- CD34- CD36- CD56- CD123- TCRγ/δ- HLA-DR- and CD235a-) were magnetically negatively isolated from peripheral blood. Cells were stimulated with anti-CD3/anti-CD28 antibodies plus IL-2, and samples were taken at 6h, 24h, 48h and 6d of stimulation. Mock stimulation control cells (sample group G02) received no further compounds, whereas induced regulatory T cells (iTregs) were either differentiated under addition of TGF-b (sample group G03) or TGF-b + retinoic acid + rapamycin (sample group G05). As control, naïve CD4+ T cells were left unstimulated (0h; sample group G01). Ex vivo isolated CD25-high cells were included as positive control for the Treg signature (“nTreg”; sample group G07). Tregs were defined by expression of FOXP3, the “master” transcription factor of Tregs. Samples from 3 male healthy donors (age 34 to 38 years) were prepared with the Qiagen Allprep kit and protein precipitate was solubilized (5 min, 95°C) in freshly prepared buffer containing 4% (w/v) SDS, 25 mM HEPES pH 7.6, 1mM DTT. Samples were prepared using the FASP assay and peptides were labeled with TMT 10-plex reagents and MS data acquired on a Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer. Phenotyping, stability and functional analyses for iTregs induced under these conditions are available in Schmidt A et al., PLoSONE 2016, PMID: 26886923). In the publication associated to this dataset, the time-course proteomic profiling during human Treg differentiation is presented and integrated with RNA-Seq data from the same cells (including additional iTreg culture conditions and 2h time points for RNA-Seq). The data underwent clustering, network analysis and disease enrichment, which revealed many known regulators of Tregs along with novel candidate genes putatively involved in FOXP3 induction, the biological importance of which was validated with a targeted shRNA screen.
HostingRepository	jPOST
AnnounceDate	2018-04-10
AnnouncementXML	Submission_2022-09-18_02:41:52.582.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Henrik Johansson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; TMT6plex reporter+balance reagent N-acylated residue; TMT6plex reporter+balance reagent acylated N-terminal
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-01-12 05:30:25	ID requested
1	2018-04-09 08:00:06	announced
2	2018-09-10 06:25:16	announced	Updated PubMed.
3	2018-09-18 23:51:17	announced	Updated CV, FTP location and Modification list.
4	2021-02-04 17:24:48	announced	2021-02-04: Updated FTP location.
⏵ 5	2022-09-18 02:41:53	announced	2022-09-18: Updated FTP location.

Schmidt A, Marabita F, Kiani NA, Gross CC, Johansson HJ, É, li, á, s S, Rautio S, Eriksson M, Fernandes SJ, Silberberg G, Ullah U, Bhatia U, L, ä, hdesm, ä, ki H, Lehti, ö J, Gomez-Cabrero D, Wiendl H, Lahesmaa R, Tegn, é, r J, Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3. BMC Biol, 16(1):47(2018) [pubmed]

submitter keyword: CD4+ T cells, Treg, IL-2, TGF-b, retinoic acid, rapamycin, TMT, time-course

Janne Lehtiö
lab head
Henrik Johansson
contact affiliation	Karolinska Institutet
dataset submitter

jPOST dataset URI

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.jpostdb.org/JPST000224/