|
| Status |
Public on Jan 21, 2019 |
| Title |
OCI-P5X miR-181a high-n3 |
| Sample type |
RNA |
| |
|
| Source name |
OCI-P5X miR-181a high
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: high-grade serous ovarian carcinoma (HGSOC) cell line
cell line: OCI-P5X miR-181a high
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell lysates of OCI-P5X miR-181a high and OCI-P5X miR-181a low cells in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry.
|
| Label |
biotin
|
| Label protocol |
In brief, for the WT Plus assay, 150ng of total RNA was labeled using a reverse transcription priming method to prime the entire length of each RNA transcript, including both polyA and non-polyA mRNA to provide complete and unbiased transcriptome coverage. This protocol efficiently generated amplified and biotinylated sense-stranded DNA targets, avoiding loss of specificity due to antisense strand interference. Data was check for quality before being assessed on the Affymetrix Clariom S Human MicroArray. Changes in mRNA expression were then identified using the Clariom S Human MicroArray. On this array expression for each gene was assessed by approximately 11 probes, which were tiled throughout the transcript. The array provides basic gene level coverage of known genes.
|
| |
|
| Hybridization protocol |
Labeled samples were hybridized to the arrays overnight in a rotating Hybridization Oven.
|
| Scan protocol |
Arrays were stained and washed in Affymetrix FS45U Fluidics Stations according to Affymetrix automated procedures.
|
| Description |
dif-a18003.dif-a1-10.rma-gene-full-Signal
|
| Data processing |
Data is collected using the GC3000 scanner with autoloader. The Clariom S Assays for the microarray data were downloaded. The data was pre-processed with RMA (Robust multichip average algorithm) using the R/Bioconductor package Oligo (42) where background subtraction, quantile normalization, and summarization (via median-polish) was accomplished.
|
| |
|
| Submission date |
Nov 29, 2018 |
| Last update date |
Jan 21, 2019 |
| Contact name |
Analisa DiFeo |
| E-mail(s) |
adifeo@med.umich.edu
|
| Organization name |
The University of Michigan
|
| Department |
Pathology
|
| Street address |
1600 Huron Parkway
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48105 |
| Country |
USA |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE123121 |
A miRNA-mediated approach to dissect the complexity of tumor-initiating cell function and identify miRNA-targeting drugs |
|
