Proteomic and phosphoproteomic comparison of human ES and iPS cells
Douglas H. Phanstiel,Justin Brumbaugh,Justin Brumbaugh,Craig D. Wenger,Shulan Tian,Mitchell D. Probasco,Derek J. Bailey,Danielle L. Swaney,Mark A. Tervo,Jennifer M. Bolin,Victor Ruotti,Ron Stewart,James A. Thomson,James A. Thomson,James A. Thomson,Joshua J. Coon +15 more
Reads0
Chats0
TLDR
Deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate is reported and the Stem Cell–Omics Repository is introduced, a resource to collate and display quantitative information across multiple planes of measurement, including mRNA, protein and post-translational modifications.Abstract:
Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very large set of identified proteins and phosphorylation sites in pluripotent cells. The statistical analysis afforded by our approach revealed subtle but reproducible differences in protein expression and protein phosphorylation between embryonic stem cells and induced pluripotent cells. Merging these results with RNA-seq analysis data, we found functionally related differences across each tier of regulation. We also introduce the Stem Cell-Omics Repository (SCOR), a resource to collate and display quantitative information across multiple planes of measurement, including mRNA, protein and post-translational modifications.read more
Citations
More filters
Journal ArticleDOI
Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks
Marco Benevento,Peter D. Tonge,Mira C. Puri,Mira C. Puri,Samer M.I. Hussein,Nicole Cloonan,David L. A. Wood,Sean M. Grimmond,Andras Nagy,Andras Nagy,Javier Muñoz,Albert J. R. Heck +11 more
TL;DR: A quantitative mass spectrometry-based analysis is performed to probe in-depth dynamic proteome changes during somatic cell reprogramming and identifies post-transcriptionally regulated proteins involved in key steps during reprograming.
Journal ArticleDOI
NANOG Is Multiply Phosphorylated and Directly Modified by ERK2 and CDK1 In Vitro
Justin Brumbaugh,Jason D. Russell,Pengzhi Yu,Michael S. Westphall,Joshua J. Coon,James A. Thomson +5 more
TL;DR: Using MAKS, site-specific phosphorylation by ERK2 and CDK1/CyclinA2 is discovered, providing a putative link between key signaling pathways and NANOG.
Journal ArticleDOI
A combined approach for single-cell mRNA and intracellular protein expression analysis.
Johan Reimegård,Marcel Tarbier,Marcus Danielsson,Jens Schuster,Sathishkumar Baskaran,Styliani Panagiotou,Niklas Dahl,Marc R. Friedländer,Caroline J. Gallant +8 more
TL;DR: SPARC as discussed by the authors is an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells and demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states.
Journal ArticleDOI
MOGSA: Integrative Single Sample Gene-set Analysis of Multiple Omics Data.
Chen Meng,Azfar Basunia,Bjoern Peters,Amin Moghaddas Gholami,Bernhard Kuster,Aedín C. Culhane +5 more
TL;DR: A new computation method termed multi-omics gene-set analysis (MOGSA), a multivariate single sample gene- set analysis method that integrates multiple experimental and molecular data types measured over the same set of samples is introduced.
Journal ArticleDOI
The human proteome - A scientific opportunity for transforming diagnostics, therapeutics, and healthcare
Marc Vidal,Daniel W. Chan,Mark Gerstein,Matthias Mann,Gilbert S. Omenn,Danilo A. Tagle,Salvatore Sechi +6 more
TL;DR: The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
Kazutoshi Takahashi,Koji Tanabe,Mari Ohnuki,Megumi Narita,Tomoko Ichisaka,Kiichiro Tomoda,Shinya Yamanaka +6 more
TL;DR: It is demonstrated that iPS cells can be generated from adult human fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc.