|
| Status |
Public on Sep 23, 2022 |
| Title |
GIST_882, 21#1shRNA-3BP2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Gastrointestinal Stromal Tumor cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GIST_882
cell type: GIST
phenotype: Imatinib sensitive
treatment: SH3BP2 shRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with a miRCURY RNA Isolation Kit (Exiqon) from NT control and SH3BP2 knockdown GIST cells
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA integrity was determined by gel electrophoresis.
|
| Label |
Hy3
|
| Label protocol |
RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent labels, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark), following the procedure described by the manufacturer
|
| |
|
| Channel 2 |
| Source name |
reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with a miRCURY RNA Isolation Kit (Exiqon) from NT control and SH3BP2 knockdown GIST cells
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA integrity was determined by gel electrophoresis.
|
| Label |
Hy5
|
| Label protocol |
RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent labels, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark), following the procedure described by the manufacturer
|
| |
|
| |
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0.
Raw dat files: Cy3 is 1_Exiqon*txt, Cy5 is 0_Exiqon*txt.
|
| Scan protocol |
The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA), and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10, see (Ritchie et al., 2007) and normalized using the global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm.
|
| |
|
| Submission date |
Sep 20, 2022 |
| Last update date |
Sep 23, 2022 |
| Contact name |
Margarita Martin |
| E-mail(s) |
martin_andorra@ub.edu
|
| Phone |
934024541
|
| Organization name |
University of Barcelona
|
| Department |
Biomedicine
|
| Street address |
Casanova 143
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21599 |
| Series (1) |
| GSE213777 |
MiRNAs array after SH3BP2 silencing in Gastrointestinal stromal tumor cells |
|
