|
| Status |
Public on Jun 03, 2019 |
| Title |
gene_expression_HIVpos_DLBCL_pt30 |
| Sample type |
RNA |
| |
|
| Source name |
DLBCL
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: pt30
tissue: Diffuse Large B-Cell Lymphoma (DLBCL)
tissue preparation: FFPE
specimen site: Rt neck mass
hiv status: HIV positive
Sex: Male
age (yrs): 36
coo: GCB
fov: 543
binding density: 0.18
|
| Treatment protocol |
One 5mm and two 10mm sections were cut from each FFPE tissue block. H&E staining was performed on the 5mm section. H&E stained sections were reviewed by a hematopathologist to confirm diagnosis and assess tumor content (tumors with <70% were macrodissected)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Allprep DNA/RNA FFPE kit (cat#80204) was used to extract total mRNA and DNA from FFPE sections as per manufacturer guidelines found here. No more than two 10mm sections were applied to a single spin column.
|
| Label |
Biotin capture probe, fluorescent barcoded reporter probe
|
| Label protocol |
300 ng of total RNA was hybridized for 12-20 hours at 65°C with the NanoString biotin labeled capture and flourescent barcoded reporter codesets as described here.
|
| |
|
| Hybridization protocol |
The now hybridized RNA/capture/reporter complexes are loaded onto the automated nCounter Prep Station where it is bound to the stredavidin coated glass cartridge via the biotin labeled capture probe.
|
| Scan protocol |
Once the RNA/capture/reporter complex is bound to the glass cartridge, the cartridge is transferred to the nCounter Digital Analyzer. An E-field orientates RNA complexes for imaging. Up to 555 fields of view (FOV) are imaged and the flourescent barcodes are enumerated.
|
| Description |
The commerical PanCancer Pathways panel was customised with the addition of 9 genes. This necessitated two RLF files, which were merged prior to running samples on the nCounter system. PanCancer rlf file = NS_CANCERPATH_C2535. BCL2 spike-in rlf file = PLS_SCHATZ_C5316
RLF File version: 1.7
|
| Data processing |
Expression data was extracted and QC'd using nSolver 3.0. Using the internal NanoString negative controls, the 99% CI threshold was determined and the data normalized as described and demonstrated in this webinar.
The sample table data is the QC'd and normalised data used to perform differential expression analysis using the statistical method NanoStringDiff described here.
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Jun 03, 2019 |
| Contact name |
Alanna Maguire |
| E-mail(s) |
[email protected]
|
| Organization name |
Mayo Clinic
|
| Department |
Research
|
| Lab |
CRB 1-250A
|
| Street address |
13400 East Shea Blvd
|
| City |
Scottsdale |
| State/province |
Arizona |
| ZIP/Postal code |
85259 |
| Country |
USA |
| |
|
| Platform ID |
GPL25534 |
| Series (2) |
| GSE119534 |
Enhanced DNA repair and genomic stability identify a novel HIV related Diffuse Large B-cell Lymphoma subtype [nanostring] |
| GSE119537 |
Enhanced DNA repair and genomic stability identify a novel HIV related Diffuse Large B-cell Lymphoma subtype |
|
