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| Status |
Public on Mar 20, 2013 |
| Title |
Comparison of stem-cell derived retinal pigment epithelia (RPE) with human fetal retina pigment epithelium |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Retinal Pigment Epithelium (RPE) derived from two human embryonic stem cell lines, H1 and H9, were compared with human fetal RPE (hfRPE) using RNA-seq. Nominally, the transcriptome of H1-derived RPE showed greater overlap with hfRPE. For cells maintained in the medium used to differentiate RPE, 6.2% (H1-RPE) and 4.2% (H9-RPE) of the transcripts were expressed in amounts that were statistically different from hfRPE (false discovery rate: 5%). After adaptation to the serum-free medium, SFM-1, only 1.0 % (H1-RPE) and 1.9% (H9-RPE) were expressed in amounts that were statistically different. For RPE signature genes, statistical differences were observed for 1.0 % (H1-RPE) and 1.9% (H9-RPE) of the transcripts. For some barrier-function related mRNAs the statistical differences were greater than these small differences would predict. For adhesion proteins and plasma membrane transporters, the differences were as great as 6.9% and 4.3%, respectively. After adaptation to SFM-1, the statistical differences between H1- and H9-RPE were only 0.4% for all transcripts, 1.4% for signature genes, and 0.7% for membrane transporters. No statistical differences were observed for the transcripts related to tight junctions, adhesion junctions or ion channels. In summary, SFM-1 promoted the maturation of stem cell-derived RPE, and the statistical difference between two stem cell lines was minimal.
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| Overall design |
RNA sequencing of hfRPE from three fetuses (reference sample) and three independent isolates of RPE derived from the H1, and three from the H9, human embryonic stem cell (hESC) lines. The cultures were maintained in a serum-free medium, SFM-1. Comparisons were also made to cultures maintained in the medium used to differentiate the cells, KSR.
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| Contributor(s) |
Rizzolo LJ, Peng S, Gan G, An H, Zhong M |
| Citation(s) |
23734062 |
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| Submission date |
Mar 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Mei Zhong |
| E-mail(s) |
mei.zhong@yale.edu
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| Phone |
203-737-6203
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| Fax |
203-785-4305
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| URL |
http://stemcell.yale.edu/index.aspx
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| Organization name |
Yale University
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| Department |
Stem Cell Center
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| Lab |
Genomics Core
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| Street address |
10 Amistad Street
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| City |
New Haven |
| ZIP/Postal code |
06510 |
| Country |
USA |
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| Platforms (2) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| SRA |
SRP011895 |
| BioProject |
PRJNA153617 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE36695_H1H9KSR_SFM.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE36695_H1H9KSR_hfSFM.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE36695_H1KSR_H1SFM.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE36695_H1SFM_H9SFM.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE36695_H1SFM_hfSFM.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE36695_H9KSR_H9SFM.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE36695_H9KSR_hfSFM.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE36695_H9SFM_hfSFM.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE36695_RAW.tar |
8.8 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE36695_gene_comparison.summary.txt.gz |
181.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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