PXD014553

PXD014553 is an original dataset announced via ProteomeXchange.

Title	Comprehensive Identification of Soybean Long Non-coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts
Description	Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-seq data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ~69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the current inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames (ORFs) from being regarded as protein-coding.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:03:09.215.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	WENGUI LIN
SpeciesList	scientific name: Glycine max; NCBI TaxID: 3847;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-10 02:54:12	ID requested
1	2020-01-09 09:48:53	announced
⏵ 2	2024-10-22 04:03:11	announced	2024-10-22: Updated project metadata.

10.1104/pp.19.01324;

Lin X, Lin W, Ku YS, Wong FL, Li MW, Lam HM, Ngai SM, Chan TF, Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts. Plant Physiol, 182(3):1359-1374(2020) [pubmed]

curator keyword: Biological

submitter keyword: long non-coding RNA, proteomics,Soybean, small peptide, transcriptomics

Sai Ming Ngai
contact affiliation	The Chinese University of Hong Kong
contact email	smngai@cuhk.edu.hk
lab head
WENGUI LIN
contact affiliation	The Chinese University of Hong Kong
contact email	guierlin@gmail.com
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/2020/01/PXD014553

PRIDE project URI

• PRIDE
  1. PXD014553
     1. Label: PRIDE project
     2. Name: Comprehensive Identification of Soybean Long Non-coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts