|
| Status |
Public on Sep 28, 2022 |
| Title |
Pre patient 4 [Sample 35] |
| Sample type |
RNA |
| |
|
| Source name |
primary high grade serous ovarian cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary high grade serous ovarian cancer biopsy
histology: high grade serous ovarian cancer
Stage: IIIC
Sex: female
age: 69
platinum-free interval: 9
progression status as of 4/25/22: yes
|
| Treatment protocol |
patients samples were obtained from naïve tumors during biopsy, or during interval debulking sugery after neoadjuvant treatment with carboplatin and paclitaxel chemotherapy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pre-treatment and post-treatment cases were reviewed to select an optimal formalin-fixed, paraffin-embedded tissue block for each case. An optimal pre-treatment block contained maximum tumor cellularity (minimum of 20%) with no lymph node tissue present. An optimal post-treatment block contained maximum tumor cellularity (minimum of 20%) with no lymph node tissue present, and with evidence of a lymphocytic response. For each block, ten unstained sections of 4-5 micron thickness were cut and placed on Avantix uncharged slides. An eleventh slide was cut at 4-5 microns, stained with hematoxylin and eosin, cover-slipped and reviewed to confirm the appropriate tissue was still present. FFPE sections were scraped into tubes for RNA isolation using an RNeasy FFPE Kit (Qiagen, 73504) according to manufacturer’s instructions. RNA concentration and quality was measured by NanoDrop
|
| Label |
fluorescent barcode
|
| Label protocol |
n/a
|
| |
|
| Hybridization protocol |
The reporter code set and capture probe set tubes were removed from -80C and thawed on ice, prior to mixing by tapping and pulse centrifugation. 70 µl hybridization buffer was added to the tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 8 µl of the diluted reporter probe was added to a PCR tube. Each RNA sample was diluted in water to 25 ng/µl and 2 µl final volume for 50 ng total input per sample. 5 µl RNA sample was added to each tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 2 µl Capture Probe Set was added to each tube, mixed by tapping, and the sample was collected by pulse centrifugation and then immediately placed in a pre-heated PCR machine, with the lid set to 70 °C and the block set to 65 °C. The hybridization was performed for 18 h at 65 °C. Samples were cooled to 4 °C and any condensation was collected by pulse centrifugation. Each sample was diluted with 18 µl hybridization buffer.
|
| Scan protocol |
An nCounter Sprint cartridge was calibrated to room temperature for 15 min prior to injection of 33 µl of each sample into one of the 12 injection ports of the cartridge, followed by the introduction of an air seal. The sample injection cartridge was sealed with provided tape and the reagent supply ports were unsealed prior to loading on the nCounter Sprint profiler. The analysis run was started immediately after loading.
|
| Description |
low count genes were filtered out for a total of 750 genes detected on the panel
|
| Data processing |
The resulting data file in RCC format was used for data analysis in the nCounter Advanced Analysis Software. Raw data in RCC format was uploaded to nSolver for automated normalization, background subtraction, and quality control (QC) check.
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Jennifer Renee Ribeiro |
| E-mail(s) |
[email protected]
|
| Organization name |
Women and Infants Hospital of Rhode Island
|
| Department |
Obstetrics and Gynecology
|
| Street address |
200 Chestnut St.
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL27956 |
| Series (1) |
| GSE201600 |
Immunologic adapatations of high grade serous ovarian cancer patients to neoadjuvant carboplatin and paclitaxel therapy |
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