ID
45815
Description
Principal Investigator: Todd E. Scheetz, PhD, The University of Iowa, Iowa City, IA, USA MeSH: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001151 Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. While much is known about the distribution of cell types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue. Datasets such as these can be used to prioritize candidate genes for possible involvement in retinal diseases with regional phenotypes. Reprinted from Whitmore, S.S., Wagner, A.H., DeLuca, A.P., Drack, A.V., Stone, E.M., Tucker, B.A., Zeng, S., Braun, T.A., Mullins, R.F., Scheetz, T.E., 2014. Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. Experimental Eye Research. Used under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported license. Additional RNA sequencing was performed on temporal, macular, nasal, inferior, and superior retina from a fifth subject and is included in this dataset. See original publication for details.
Link
Keywords
Versions (1)
- 6/29/23 6/29/23 - Simon Heim
Copyright Holder
Todd E. Scheetz, PhD, The University of Iowa, Iowa City, IA, USA
Uploaded on
June 29, 2023
DOI
To request one please log in.
License
Creative Commons BY 4.0
Model comments :
You can comment on the data model here. Via the speech bubbles at the itemgroups and items you can add comments to those specificially.
Itemgroup comments for :
Item comments for :
In order to download data models you must be logged in. Please log in or register for free.
dbGaP phs001151 Region-specific Transcriptome Analysis of the Human Retina and RPE/Choroid
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and case control status of the subject for retinal diseases.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample aliases and sample use.
- This subject phenotype table contains subject IDs, gender, age, and cause of death of the subject.
- This sample attributes table contains sample IDs, body site where sample was collected, analyte type, histological type, tumor status, anatomic region of retina, laterality of eye, approximate time (in hours) from death of donor to stabilization of RNA, sequencing library type, and sequencing library protocol.
Similar models
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and case control status of the subject for retinal diseases.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample aliases and sample use.
- This subject phenotype table contains subject IDs, gender, age, and cause of death of the subject.
- This sample attributes table contains sample IDs, body site where sample was collected, analyte type, histological type, tumor status, anatomic region of retina, laterality of eye, approximate time (in hours) from death of donor to stabilization of RNA, sequencing library type, and sequencing library protocol.
C0680251 (UMLS CUI [1,2])
C0025102 (UMLS CUI [1,2])