|
| Status |
Public on Feb 26, 2020 |
| Title |
AMD Patient 3 iPS RPE |
| Sample type |
RNA |
| |
|
| Source name |
AMD patient donor derived
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: AMD Patient 3
donor status: advanced age-related macular degeneration (AMD)-patient
cell type: iPS-derived retinal pigment epithelial (RPE) cells
|
| Treatment protocol |
no special treatment
|
| Growth protocol |
Fibroblasts from 4 donors with age-related macular degeneration and 3 controls with no history of AMD were grown and treated with modified messenger ribonucleic acid (mRNA) encoding reprogramming factors, Oct3/4, Sox-2, Klf4, and c-Myc, nanog and Lin28. Newly generated iPSC colonies were picked and expanded using Nutristem medium (Stemgent, Reprocell, MD, USA) or MTeSR™1 media. iPSC colonies were detached and grown as embryoid bodies (EB) in EB formation medium and STEMdiff™ Neural Induction Medium and RPE differentiation medium containing DMEM/F12, 2% B-27 supplement, minimum essential media, non-essential amino acids and antibiotics. At ~45 days, pigmented iPSC-derived RPE cells appeared in the cultures. Patches of pigmented iPSC-derived RPE cells were micro-dissected, dissociated with trypsin-ethylenediaminetetraacetic acid (EDTA, 0.05%), and plated onto laminin-coated plates until confluent as previously described.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from differentiated iPSC-derived RPE cells using Aurum™ Total RNA Mini Kit (Bio-Rad Laboratories, CA, USA) according to the manufacturer’s instructions, with Dnase I treatment. RNA quantity and quality were assessed by micro-volume spectrophotometry on the Nanodrop 2000 (Thermo Fisher Scientific) and by on-chip capillary electrophoresis on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
GeneChip® WT Plus Reagent Kit were used for generating biotinylated ss-cDNA for hybridization.
|
| |
|
| Hybridization protocol |
All reactions and hybridizations were carried out according to the manufacturer's protocol (Affymetrix; Thermo Fisher Scientific). Affymetrix GeneChip Human Clariom S arrays (Thermo Fisher Scientific) were washed using the GeneChip® Fludics Station 450 (Thermo Fisher Scientific)
|
| Scan protocol |
Affymetrix GeneChip Human Clariom S arrays were scanned with the GeneChip Scanner 3000 (Thermo Fisher Scientific).
|
| Description |
RMA expression value derived from Expression Console software Transcriptome Analysis Console (TAC) 4.0.1 (Applied Biosystems)
|
| Data processing |
Raw data were processed to perform gene-level normalization and quality control using Affymetrix Expression Console Software (Thermo Fisher Scientific). RMA expression value derived from Expression Console software Transcriptome Analysis Console (TAC) 4.0.1 (Applied Biosystems)
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.na36.hg38.a1.transcript.csv
Normal vs AMD, Normal: 3 samples, AMD: 4 samples; Filter criteria: Fold Change: > 2 or < -2; Total number of genes: 21448
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Apr 23, 2020 |
| Contact name |
Hui Cong Cai |
| E-mail(s) |
huey.cai@yale.edu
|
| Organization name |
Yale University
|
| Street address |
300 George St, Suite 8100
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06011 |
| Country |
USA |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE125564 |
Reduced extracellular matrix survival and altered metabolic activity in iPSC-derived RPE cells from AMD patients |
|
| Relations |
| Reanalyzed by |
GSM4492148 |
