PXD039006

PXD039006 is an original dataset announced via ProteomeXchange.

Title	Circadian Gene Expression in Mouse Renal Proximal Tubule
Description	Circadian variability in kidney function has long been recognized but is often ignored as a potential confounding variable in in vivo physiological experiments. To provide a guide for physiological studies on the kidney proximal tubule, we have now created a data resource consisting of expression levels for all measurable mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. This approach employs small-sample RNA-sequencing (RNA-seq) applied to microdissected renal proximal tubules including both S1 proximal convoluted tubules (PCTs) and S2 proximal straight tubules (PSTs). The data were analyzed using JTK-Cycle to detect periodicity. The data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox/. In PCTs, 234 transcripts were found to vary in a circadian manner (3.7 % of total quantified). In PSTs, 334 transcripts were found to vary in a circadian manner (5.3 % of total quantified). Transcripts previously known to be associated with corticosteroid action and transcripts associated with increased flow were found to be overrepresented among circadian transcripts peaking during the “dark” portion of the day (Zeitgeber 14-22), corresponding to the peak levels of corticosterone and glomerular filtration rate in mice.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:44:46.803.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	CHIN-RANG YANG
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-20 23:29:58	ID requested
1	2023-04-10 08:17:48	announced
⏵ 2	2023-11-14 08:44:48	announced	2023-11-14: Updated project metadata.

Bingham MA, Neijman K, Yang CR, Aponte A, Mak A, Kikuchi H, Jung HJ, Poll BG, Raghuram V, Park E, Chou CL, Chen L, Leipziger J, Knepper MA, Dona M, Circadian gene expression in mouse renal proximal tubule. Am J Physiol Renal Physiol, 324(3):F301-F314(2023) [pubmed]

submitter keyword: Circadian variation, proteomics, proximal tubule, transcriptomics

Mark A. Knepper
contact affiliation	Epithelial Systems Biology Laboratory Systems Biology Center Division of Intramural Research National Heart, Lung and Blood Institute Building 10, Room 6N307 Bethesda, Maryland 20895-1603
contact email	knepperm@nhlbi.nih.gov
lab head
CHIN-RANG YANG
contact affiliation	National Institutes of Health, USA
contact email	chin-rang.yang@nih.gov
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/2023/04/PXD039006

PRIDE project URI

• PRIDE
  1. PXD039006
     1. Label: PRIDE project
     2. Name: Circadian Gene Expression in Mouse Renal Proximal Tubule