PXD008693

PXD008693 is an original dataset announced via ProteomeXchange.

Title	EMpire: Deep isoform level integration of the transcriptome, translatome, and proteome
Description	In this study, we make used of mRNA-seq and its ability to reliably quantify isoforms, integrating this data with ribosome profiling and LC-MS/MS, to assign ribosome footprints and peptides at the isoform level. We leverage the principle that most cell types, and even tissues, predominantly express a single principal isoform to set isoform-level mRNA-seq quantifications as priors to guide and improve allocation of footprints or peptides to isoforms. Through tightly integrated mRNAseq, ribosome footprinting and/or LC-MS/MS proteomics we demonstrate that a principal isoform can be identified in over 80% of gene products in homogenous HEK293 cell culture and over 70% of proteins detected in complex human brain tissue. Defining isoforms in experiments with matched RNA-seq and translatomic/proteomic data increases the functional relevance of such datasets and will further broaden our understanding of multi-level control of gene expression. In this PRIDE submission you will find the raw files for the HEK293 cell proteomics. Files for the human brain proteomics can be found at PXD005445. We have also uploaded a zip file that contains the input files for our HEK293 cell analysis, and the isoform level output files – there is a separate folder within the zip files for these. The data used to create the manuscript figures is in the Rdata file. Code for assigning peptides and footprints to isoforms can be found on Github here: https://github.com/rkitchen/EMpire
HostingRepository	PRIDE
AnnounceDate	2018-08-21
AnnouncementXML	Submission_2018-08-21_11:38:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	TuKiet Lam
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-16 08:51:32	ID requested
⏵ 1	2018-08-21 11:38:03	announced

Carlyle BC, Kitchen RR, Zhang J, Wilson RS, Lam TT, Rozowsky JS, Williams KR, Sestan N, Gerstein MB, Nairn AC, Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq. J Proteome Res, 17(10):3431-3444(2018) [pubmed]

curator keyword: Biological

submitter keyword: Proteomics, LC-MS/MS, Protien Isoforms, mRNA-Seq

TuKiet Tan Lam
contact affiliation	Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, PO Box 208114, New Haven, CT, 06520
contact email	tukiet.lam@yale.edu
lab head
TuKiet Lam
contact affiliation	Yale University
contact email	tukiet.lam@yale.edu
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/2018/08/PXD008693

PRIDE project URI

• PRIDE
  1. PXD008693
     1. Label: PRIDE project
     2. Name: EMpire: Deep isoform level integration of the transcriptome, translatome, and proteome