PXD046084

PXD046084 is an original dataset announced via ProteomeXchange.

Title	Dynamics and consequences of widespread transcript isoform changes during neuronal differentiation
Description	Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform change upon cell-state transitions during cell differentiation, and the determinants and functional consequences have largely remained unclear. Here, we used an improved model for human neurogenesis in vitro that we show is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct stages during neurogenesis. RNA isoforms mainly arise from the alternative usage of transcription start sites and poly-adenylation sites as well as the skipping of individual exons during human neurogenesis. The transcript isoform changes can remodel the abundance and functions of protein isoforms. Finally, our study identifies a set of RNA-binding proteins as a likely determinant of differentiation stage-specific global isoform changes.
HostingRepository	PRIDE
AnnounceDate	2024-04-11
AnnouncementXML	Submission_2024-04-11_07:25:09.898.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046084
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	David Meierhofer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-12 03:25:16	ID requested
⏵ 1	2024-04-11 07:25:10	announced

10.6019/PXD046084;

submitter keyword: cell differentiation, neurogenesis, multi-omics, RNA isoform, Nanopore sequencing

Andreas Mayer
contact affiliation	Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
contact email	mayer@molgen.mpg.de
lab head
David Meierhofer
contact affiliation	Mass Spectrometry Facility MPIMG
contact email	meierhof@molgen.mpg.de
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/2024/04/PXD046084

PRIDE project URI

• PRIDE
  1. PXD046084
     1. Label: PRIDE project
     2. Name: Dynamics and consequences of widespread transcript isoform changes during neuronal differentiation