|
| Status |
Public on Jun 20, 2023 |
| Title |
HCC-OC-002-1 |
| Sample type |
RNA |
| |
|
| Source name |
HCC patient
|
| Organism |
Homo sapiens |
| Characteristics |
subject status/id: HCC patient 2
age: 71
gender: female
hbsag: (-)
anti-hcv: (+)
afp: 67.1
dcp: 127
cea: 4.3
ca19-9: 25
tissue: peripheral blood
molecule subtype: microRNA
|
| Treatment protocol |
Peripheral blood was collected from all subjects directly into serum tubes before anti-viral treatment. The tubes were centrifuged at 1,500 g for 10 min at 4℃, sera were aliquoted and additionally centrifuged at 2,000 g to completely remove any remaining cells. Sera were stored at -80℃ until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 200 ul of serum was prepared using miRNeasy mini kit (Qiagen, Hilden Germany) according to the manufacturer’s instruction. Exosome rich fractionated RNA was prepared using Exoquick (System Biosciences, CA, USA). Briefly, 900 ul of serum was mixed with 250 ul of Exoquick and incubated for 12 hr at 4℃. The tubes were centrifuged at 1500 g for 30 min at room temperature and then supernatant was discarded. The pellet was dissolved with 200 ul of PBS with vigorous vortex. RNA was extracted using miRNeasy mini kit (Qiagen).
|
| Label |
cy3
|
| Label protocol |
To detect serum miRNA, 60 ng of RNA was labeled using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to the manufacturer’s protocol (protocol for use with Agilent microRNA microarrays Version 1.0).
|
| |
|
| Hybridization protocol |
Labeled RNA was hybridized on microarray for 20hours at 55℃ by using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to the manufacturer’s protocol (protocol for use with Agilent microRNA microarrays Version 1.0).
|
| Scan protocol |
Hybridization signals were detected with a DNA microarray scanner G2505B (Agilent Technologies) and the scanned images were analyzed using Agilent feature extraction software (v9.5.3.1).
|
| Description |
SAMPLE 20
microRNA in blood exosome of HCC patients
|
| Data processing |
Data were analyzed using the GeneSpring GX10.0.2 (Agilent). Quality control (QC) was applied according to the manufacturer’s instructions, and all data were approved by GeneSpring.
We used raw data (gProcessedSignal) and normalized each expression so as to have zero mean and unit sample variance.
|
| |
|
| Submission date |
Jun 06, 2016 |
| Last update date |
Jun 20, 2023 |
| Contact name |
Y-H. Taguchi |
| E-mail(s) |
tag@granular.com
|
| Phone |
+81-3-3817-1791
|
| Organization name |
Chuo University
|
| Department |
Physics
|
| Street address |
1-13-27 Kasuga,Bukyo-ku
|
| City |
Tokyo |
| State/province |
Non-US/Canada |
| ZIP/Postal code |
112-8551 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14943 |
| Series (2) |
| GSE82302 |
Blood exsosomal miRNAs of liver disease patients |
| GSE82303 |
Blood exsosomal miRNAs of patients with normal livers and liver disease patients |
|
