Project PXD003903

PRIDE Assigned Tags:
Biomedical Dataset Biological Dataset

Summary

Title

HipSci project pilot submission for 18 IPS cell lines

Description

The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Associated BioSamples accessions: SAMEA2397999, SAMEA2398167, SAMEA2398916, SAMEA2397948 , SAMEA2399112,SAMEA2399257, SAMEA2398553, SAMEA2398821, SAMEA2398316, SAMEA2469778, SAMEA2399037, SAMEA2398656, SAMEA2398428, SAMEA2469777, SAMEA2397959, SAMEA2398442, SAMEA2398024, SAMEA2398450, SAMEA3402864, SAMEA3110364

Sample Processing Protocol

The frozen iPS cell pellets were solubilized using lysis buffer (8M urea, 100 mM TEAB). The cell lysates were digested using a two-step digestion protocol (overnight Lys-C digestion followed by 4 hour-tryptic digestion). Strong Anion eXchange (SAX) chromotography was used to fractionate the peptides for subsequent LC-MS/MS analyses.

Data Processing Protocol

Proteomics analyses were performed using Q-exactive mass spectrometer and the data processing were carried out using Maxquant version 1.3.0.5. Data were processed with the following settings: 2 missed cleavages allowed, enzyme used was trypsin/P, 20 ppm tolerance was used for fragment ions, FDR cut off of 0.5 was used. One fixed modification: carbamidomethylation (Cys), and few variable modifications were selected: Oxidation (M); Acetylation (N-term), deamidation (NQ), pyroglutamate conversion of glutamine.

Contact

HipSci Project, Human Induced Pluripotent Stem Cells Initiative Human Induced Pluripotent Stem Cells Initiative Human Induced Pluripotent Stem Cells Initiative
Angus Lamond, College of Life Sciences, University of Dundee ( lab head )

Submission Date

06/06/2016

Publication Date

06/06/2016

Corresponding dataset(s) in other omics resources

SAMEA2397999 (ENA, EMBL-EBI)
SAMEA2398167 (ENA, EMBL-EBI)
SAMEA2398916 (ENA, EMBL-EBI)
SAMEA2397948 (ENA, EMBL-EBI)
SAMEA2399112 (ENA, EMBL-EBI)
SAMEA2399257 (ENA, EMBL-EBI)
SAMEA2398553 (ENA, EMBL-EBI)
SAMEA2398821 (ENA, EMBL-EBI)
SAMEA2398316 (ENA, EMBL-EBI)
SAMEA2469778 (ENA, EMBL-EBI)
SAMEA2399037 (ENA, EMBL-EBI)
SAMEA2398656 (ENA, EMBL-EBI)
SAMEA2398428 (ENA, EMBL-EBI)
SAMEA2469777 (ENA, EMBL-EBI)
SAMEA2397959 (ENA, EMBL-EBI)
SAMEA2398442 (ENA, EMBL-EBI)
SAMEA2398024 (ENA, EMBL-EBI)
SAMEA2398450 (ENA, EMBL-EBI)
SAMEA3402864 (ENA, EMBL-EBI)
SAMEA3110364 (ENA, EMBL-EBI)

Publication

    Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature. 2017 May 10 PubMed: 28489815