PXD068030

PXD068030 is an original dataset announced via ProteomeXchange.

Title	Comparison of Transcript and Protein Abundance in Human Donor Retinas Support Extending Post-Mortem Interval from 12- to 18-hours to Expand the Donor Pool for Biomedical Research
Description	Extending the post-mortem interval (PMI) from 12- to 18-hours was done to see if transcript and protein abundance in the human retina changed. Donor eyes were recovered from post-mortem donors (n=7 pairs) and stored at 2–8°C. Only donor eyes with ocular cooling within 8 hours of death were examined. The OD retina was preserved at 12 hours and the OS retina at 18 hours post-mortem. Retinas were flash frozen with liquid nitrogen. The macular region superior to the fovea was used for RNA sequencing (RNA-seq). RNA library preparations were performed simultaneously, and the sequencing of all samples were conducted on the same chip. The inferior region was processed for isobaric labeling (TMT) quantitative mass spectrometry. Proteins were isolated from samples and labeled with 16-plex TMTPro isobaric tags. RNA-seq data were processed using DESeq2 (Bioconductor) and proteomic data were analyzed using the OHSU Comet/PAW pipeline. RNA-seq identified 22,446 transcripts, with only 5 transcripts showing significant differential expression (adjusted-P<0.1 and a Log2FoldChange>1) between 12 and 18 hours. Proteomic analysis identified 6,109 proteins, with no significant differences in abundance (all adj-P > 0.05, 1% FDR). Retinal cell-type specific markers and markers relevant for disease research, such as age-related macular degeneration and glaucoma, remained stable across both collection time points. Extending the PMI cutoff from 12 to 18 hours did not significantly impact transcriptomic or proteomic integrity in human donor retinas. This collection period extension greatly increases the availability of donor eyes for biomedical research.
HostingRepository	PRIDE
AnnounceDate	2026-04-07
AnnouncementXML	Submission_2026-04-07_13:42:50.868.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Phillip Wilmarth
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-03 03:56:11	ID requested
⏵ 1	2026-04-07 13:42:51	announced

10.1167/iovs.67.4.9;

Easton CA, Wilmarth PA, Criss M, Kim K, Reddy AP, Tanne S, Boone JQ, Tran KD, Comparison of Transcript and Protein Abundance in Human Donor Retinas Support Extending Postmortem Interval From 12 to 18 Hours to Expand the Donor Pool for Biomedical Research. Invest Ophthalmol Vis Sci, 67(4):9(2026) [pubmed]

submitter keyword: TMTpro, mass spectrometry,Retina, Orbitrap Tribrid SPS-MS3 acquisition, donor collection time, isobaric labeling quantitative proteomics

Khoa D. Tran
contact affiliation	VisionGift, Research 2201 SE 11th Ave Portland, Oregon 97214 USA
contact email	Khoa@visiongift.org
lab head
Phillip Wilmarth
contact affiliation	OHSU
contact email	wilmarth@ohsu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD068030
     1. Label: PRIDE project
     2. Name: Comparison of Transcript and Protein Abundance in Human Donor Retinas Support Extending Post-Mortem Interval from 12- to 18-hours to Expand the Donor Pool for Biomedical Research