PXD010282

PXD010282 is an original dataset announced via ProteomeXchange.

Title	Extensive OMICS resources for Sf21 and High Five cell lines
Description	Insect derived cell-lines, from Spodoptera frugiperda (Sf21) and from Trichoplusia ni (High Five), are ones of the most widely used systems for recombinant protein expression in Baculoviral Expression Vector System (BEVS). Genomic sequences and annotations are still incomplete for Sf21 or absent for High Five. In this study we present an approach using different sequencing data types with short-read sequencing, long synthetic and Oxford Nanopore reads to build genomes at an unprecedented resolution. The Sf21 and High Five assemblies contain 4,020 scaffolds of size, 463 Mb with N50 of 364 Kb and 2,954 scaffolds of size, 332 Mb with N50 of 326 Kb, respectively. Furthermore, we build a new gene prediction workflow, which integrates transcriptome proteome information using pre-existing tools. Using this approach, we could predict 21,506 Sf21 genes and 14,159 High Five genes, which were then functionally annotated. Finally, we also generate and integrate proteomic datasets to validate predicted genes. This integrative approach could be theoretically applied to any uncharacterized genome and result in valuable new resources. With this information available, Sf21 and High Five cells will become even better tools for protein expression and could be used in a wider range of applications, from promoter identifications to genome engineering and editing.
HostingRepository	PRIDE
AnnounceDate	2022-03-03
AnnouncementXML	Submission_2022-03-03_02:40:23.088.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joanna Kirkpatrick
SpeciesList	scientific name: Spodoptera frugiperda; NCBI TaxID: 7108; scientific name: Trichoplusia ni; NCBI TaxID: 7111;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-02 04:08:26	ID requested
⏵ 1	2022-03-03 02:40:23	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: insect cell lines, Sf21, High Five, genomic, proteomic, transcriptomic

Vladimir Benes
contact affiliation	Head of Genomics Core Facility EMBL Scientific Core Facilities, Services & Technology Unit Meyerhofstr. 1 D-69117 Heidelberg Germany
contact email	benes@embl.de
lab head
Joanna Kirkpatrick
contact affiliation	Leibniz Institute on Aging - FLI
contact email	joanna.kirkpatrick@leibniz-fli.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/2022/03/PXD010282

PRIDE project URI

• PRIDE
  1. PXD010282
     1. Label: PRIDE project
     2. Name: Extensive OMICS resources for Sf21 and High Five cell lines