|
| Status |
Public on Apr 04, 2019 |
| Title |
RNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by RT-PCR
|
| Summary |
We developed a novel approach to isolate tumor cells with high purity from bone marrow which was subjected to immunomagnetic enrichment using EpCAM beads followed by fluorescence activated cell sorting (IE/FACS) to isolate EpCAM-positive cells away from leukocytes (CD45+).
For RNA profiling, QPCR analysis was performed on sixty four (64) cancer-related genes using Taqman® low density arrays. For non-tumor controls, RNA profiling was performed on matched leukocytes (CD45+) isolated from the same enriched bone marrow samples from 17 of the 30 patients.
|
| |
|
| Overall design |
Bone Marrow aspirates where taken from EBC patients. Patients were considered positive (DTC≥1 cell/ml) via immunomagnetic enrichment followed by flow cytometry (IE/FC). When a sample was determined positive, the remainder of the bone marrow was processed and sorted via IE/FACS. 36 aspirates where sorted for RNA analysis. Quality control (QC) measures were implemented as follow: Sorted cells ≥10, expression of house keeping genes RPS18 and ACTB (Ct value ≤26 and ≤36 respectively), and detection rate ≥ 20% of 64 gene panel. 31 samples from 30 patients passed all QC.
|
| |
|
| Contributor(s) |
Magbanua MM, Hauranieh L, Sosa EV, Roy R, Eisenbud LE, Scott JH, Olshen A, Pinkel D |
| Citation(s) |
30211312 |
| |
| Submission date |
Apr 05, 2018 |
| Last update date |
May 16, 2019 |
| Contact name |
Mark Magbanua |
| Organization name |
UCSF/Helen Diller Familiy Comprehensive Cancer Center
|
| Department |
HemOnc
|
| Lab |
Park
|
| Street address |
1450 3rd Street, PO Box 589001
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158-9001 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16020 |
Applied Biosystems TaqMan TLDA 64-Breast cancer associated-gene panel |
|
| Samples (45)
|
|
| This SubSeries is part of SuperSeries: |
| GSE112759 |
Parallel DNA and RNA profiling of EpCAM-positive cells in bone marrow and primary tumor tissue with positive disseminated tumor cell count via immunomagnetic Enrichment/Flow Cytometry of metastatic breast cancer patients confirm their malignant nature |
|
| Relations |
| BioProject |
PRJNA448910 |
Less...
More...