|
| Status |
Public on Aug 21, 2019 |
| Title |
Tumor 1 |
| Sample type |
RNA |
| |
|
| Source name |
homo sapiens colon
|
| Organism |
Homo sapiens |
| Characteristics |
patient diagnosis: Stage IIIA Colon Cancer
Sex: male
tissue: colon tumor tissue
|
| Growth protocol |
Both control and tumor tissues of around 0.5 cm3 in size, collected from patients for the study were preserved at -80 °C in 200 ml RNAlater solution. GeneChip miRNA 4.0 Array (Affymetrix, USA) was used for this study, according to the manufacturer’s protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNAs were isolated from tissue samples that were homogenized in QIAzol (Qiagen, Germany) at 4 C°, by using Qiagen miRNeasy (Qiagen, Germany) mini kit. The quality of isolated RNAs was measured using a nano spectrophotometer (Implen, Germany).
|
| Label |
biotin
|
| Label protocol |
Briefly, 1 μg of RNA was labeled using a FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, USA).
|
| |
|
| Hybridization protocol |
The labeled RNA samples were loaded onto microarray chips and hybridization was performed with continuous agitation using a GeneChip Hybridization Control Kit (Affymetrix, USA) at 48 °C at 60 rpm for 16 h
|
| Scan protocol |
Then, microarray chips were washed and stained on a Fluidics Station 450 with AGCC Fluidics Control Software. Fluorescence from the array was scanned using an Affymetrix® GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, USA).
|
| Data processing |
Finally, the hybridization data (CEL files) was normalized by the Affymetrix GeneChip Command Console software and imported into probe-level summarization files (*CHP files) for data extraction. Analyses of these CHP files were performed using Affymetrix® GeneChip Command Console® Software (AGCC)
|
| |
|
| Submission date |
Aug 20, 2019 |
| Last update date |
Aug 21, 2019 |
| Contact name |
Cigdem GUNGORMEZ |
| E-mail(s) |
gungormezcigdem@gmail.com
|
| Organization name |
Harran University
|
| Street address |
HUBTAM
|
| City |
SANLIURFA |
| ZIP/Postal code |
63100 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL14613 |
| Series (1) |
| GSE136020 |
The miRNA Profile and Bioinformatic Analysis for Diagnosis in Patients with Stage IIIA Colon Cancer |
|
