PXD016339

PXD016339 is an original dataset announced via ProteomeXchange.

Title	An Integrative Transcriptome – Proteome Approach Reveals a Robust Expression Pattern of Small Intestinal Epithelial Organoids from Germ-Free and Microbiota Associated Donors
Description	Intestinal epithelial organoids established from resected gut tissue have become a widely used research tool. However, it remains unclear how environmental cues and other sources of variation before, during and after establishment impact on organoid properties. Divergent microbiota composition in separately held mouse lines has been identified as a confounding factor in murine in vivo studies. To probe the effect of donor microbiota on organoids, we analyzed the proteomes and transcriptomes of primary organoid cultures established from colonized and germ-free mice, and further compared them to their tissue of origin and to commonly used cell lines. The long-term global impact of donor microbiota on organoid expression patterns was negligible. Instead, stochastic culture-to-culture differences accounted for a moderate variability between independently established organoids. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and fibroblasts. This signature, which closely mimicked expression patterns in the gut epithelium, included high levels of the inflammasome scaffold protein ASC in organoids which was lacking in commonly used cell lines. Mining of the transcriptome dataset uncovered similar high expression of also other inflammasome components, including Naip1-6, Nlrc4, and Caspase-1 in all organoids compared to the reference cell lines. Taken together, these results reveal a robust global expression pattern in organoids established from colonized and germ-free animals and suggest that organoids represent a more suitable culture model than immortalized cell lines for studies of intestinal epithelial inflammasomes.
HostingRepository	PRIDE
AnnounceDate	2020-03-05
AnnouncementXML	Submission_2020-03-05_04:12:54.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbora Salovska
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-19 04:15:06	ID requested
⏵ 1	2020-03-05 04:12:55	announced

Hausmann A, Russo G, Grossmann J, Z, ü, nd M, Schwank G, Aebersold R, Liu Y, Sellin ME, Hardt WD, Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes. Cell Microbiol, 22(6):e13191(2020) [pubmed]

submitter keyword: Intestinal Epithelial Organoids

SWATH

5600

Yansheng Liu
contact affiliation	Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
contact email	yansheng.liu@yale.edu
lab head
Barbora Salovska
contact affiliation	Institute of Molecular Genetics of the Czech Academy of Sciences
contact email	salovska@img.cas.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016339
     1. Label: PRIDE project
     2. Name: An Integrative Transcriptome – Proteome Approach Reveals a Robust Expression Pattern of Small Intestinal Epithelial Organoids from Germ-Free and Microbiota Associated Donors