|
| Status |
Public on Aug 01, 2014 |
| Title |
Primary colon tumor GIM-01A |
| Sample type |
RNA |
| |
|
| Source name |
Primary colon tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary colon tumor
case id: GIM01
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.
|
| Label |
n/a
|
| Label protocol |
Nanostring Human MicroRNA assays v1
|
| |
|
| Hybridization protocol |
Expression analysis was performed according to the written protocol provided by NanoString Technologies (Seattle, WA). Briefly, a 5 µl aliquot containing 100 ng of denatured total RNA was added to 20 µl of master mix consisting of equal amounts of Reporter CodeSet solution and hybridization buffer. Five µl of Capture ProbeSet were added to the mix the hybridization was performed overnight at 65°C.
|
| Scan protocol |
Post-hybridization processing and scanning was performed using the nCounter analysis system at the NCI CCR DNA Sequencing and Digital Gene Expression Core Facility.
|
| Data processing |
Probe level background subtraction was applied for the 13 probes which had background hybridizations levels as indicated by the manufacturer. microRNAs are listed with their background coefficient for correction in parentheses. hsa-miR-27b (0.08) hsa-miR-133a (0.05), hsa-miR-544 (0.03), hsa-miR-320c (0.03), hsa-miR-590-5p (0.01), hsa-miR-16 (0.01), hsa-miR-494 (0.01), hsa-miR-579 (0.01), hsa-miR-193a-3p (0.005), hsa-miR-196a (0.005), hsa-miR-485-3p (0.005), hsa-miR-1283 (0.005). Data was then normalized to the geometric mean of the 75 highest expressed microRNAs. These are the first 75 microRNAs listed the normalized data.
|
| |
|
| Submission date |
Feb 06, 2013 |
| Last update date |
Aug 01, 2014 |
| Contact name |
Aaron Schetter |
| E-mail(s) |
schettera@mail.nih.gov
|
| Organization name |
National Cancer Institute
|
| Department |
Laboratory of Human Carcinogenesis
|
| Street address |
37 Convent Drive, Building 37, Room 3050
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16231 |
| Series (1) |
| GSE44121 |
Association of microRNAs with colon tumor metastases |
|
