|
| Status |
Public on Jul 07, 2023 |
| Title |
Type 2 Diabetic Retinopathy within 5 years - Clustering group B - #1 |
| Sample type |
RNA |
| |
|
| Source name |
Type-2 diabetic patient, with DR complication within 5 years, was assigned to group B by hierarchical clustering on principal components.
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
gender: Female
age: 57 years old
t2d duration: less than 1 year
hba1c (%) of the sample: 7.3%
bmi: 21.30 kg/m2
sampling t2d stage: T2D with retinopathy
reference: Changhua Christian Hospital
|
| Extracted molecule |
total RNA |
| Extraction protocol |
According to medical records of China Medical University Hospital and Changhua Christian Hospital, the selected candidates were diagnosed and classified into detailed groups non-diabetes as control, type-2 diabetes without DN/DR complications (T2D), type-2 diabetes with nephropathy (T2DN), and type-2 diabetes with retinopathy (T2DR). Based on the classifications, the blood samples of them were collected individually. Next, whole cells in the samples was accumulated by centrifugation and homogenized to prepare mixtures for RNA extraction.
Total RNA was subsequently isolated by RNeasy Mini Kit (P/N: 74104, QIAGEN) according to the manufacturer's instructions. Then, RNA quantity and purity were assessed at 260 nm and 280nm using a Nanodrop (ND-1000; Labtech. International).
|
| Label |
Biotin
|
| Label protocol |
300 ng of each sample was amplified and labeled using the GeneChip™ WT Sense Target Labeling and Control Reagents (Catalog number: 900652).
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| |
|
| Hybridization protocol |
The hydridization was performed against the Clariom™ D Assay, human (Catalog Number: 902923) by following the Affymetrix protocol for 17 hours at 45°C and 60 rpm.
|
| Scan protocol |
The arrays were subsequently washed (Affymetrix Fluidics Station 450) and stained with streptavidin-phycoerythrin(GeneChip® Hybridization, Wash, and Stain Kit, 900720), and were scanned on an Affymetrix GeneChip® Scanner 3000 7G.
|
| Data processing |
The scanning-output data, which was stored in CEL files, was analyzed by using Transcriptome Analysis Console (TAC) software of the Affymetrix company with default parameters. Moreover, uploaded CHP files were generated from the CEL files by the software.
The levels of RNA expression were determined with the Tukey biweight average scores, which was compared with eBayes, which is one of ANOVA methods, which was performanced by the TAC suite (version 4.0.2.15).
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| |
|
| Submission date |
Nov 17, 2021 |
| Last update date |
Jul 07, 2023 |
| Contact name |
Fuu-Jen Tsai |
| E-mail(s) |
d0704@mail.cmuh.org.tw
|
| Organization name |
China Medical University Hospital
|
| Department |
Department of Medical Research
|
| Lab |
Genetic Center
|
| Street address |
No.2, Yude Rd., North Dist.
|
| City |
Taichung |
| ZIP/Postal code |
40447 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL23126 |
| Series (2) |
| GSE189005 |
RNA expression profiles of whole blood cells from a Han Chinese population with or without Type-2 Diabetes Mellitus or/and its complications in nephropathy and retinopathy |
| GSE189007 |
Gene-expression profiles of whole blood cells from a Han Chinese population with or without Type-2 Diabetes Mellitus or/and its complications in nephropathy and retinopathy |
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