|
| Status |
Public on May 15, 2024 |
| Title |
Negative control blank |
| Sample type |
other |
| |
|
| Source name |
olfactory neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: olfactory neuroblastoma
|
| Extracted molecule |
other |
| Extraction protocol |
5 µm sections from high quality archival ONB tissue blocks was mounted on glass slides for profiling. Two adjacent sections were cut and positioned on separate slides to allow for side-by-side H&E comparison. Following deparaffinization, antigen retrieval was performed with Tris-EDTA buffer (pH 9.0) in a steamer for 20 min. Slides were then incubated for 15 min at 37°C in PBS buffer with 0.1 µg/mL proteinase K for RNA target exposure.
|
| Label |
n.a.
|
| Label protocol |
Slides were stained with fluorescence-conjugated morphology markers for two hr at RT with the following labels: Syto 83 nuclear dye (NanoString) 250nM, CD45-532 (NovusBio cat# NBP2-34528AF532) 7.50µg/mL, TUBB3-594 (Biolegend, cat# 657408) 1:50, KI67-647 (CST cat# 12075) 1:100.
|
| |
|
| Hybridization protocol |
In situ hybridization was conducted by incubating slides with GeoMx Human Whole Transcriptome Atlas Probe Mix (NanoString) overnight at 37°C. See Nanostring slide preparation protocol for more information: https://university.nanostring.com/geomx-dsp-manual-slide-preparation-user-manual
|
| Scan protocol |
Default settings on the Nanostring GeoMx DSP were used, see: https://university.nanostring.com/geomx-dsp-instrument-user-manual.
|
| Data processing |
Oligos were processed for library preparation according to the standard Nanostring protocol, with the exception that beads were dried for 1 min instead of 5. DNA libraries were sequenced on an Illumina NovaSeq 6000 S-Prime flow cell with a read length of 2x27bp and a 5% PhiX spike-in by volume. Output .fastq files from sequencing runs were converted to .dcc using the GeoMx NGS Pipeline with default parameters. See Nanostring protocol for more specific information: https://university.nanostring.com/geomx-dsp-ngs-readout-user-manual
|
| |
|
| Submission date |
Sep 26, 2023 |
| Last update date |
May 15, 2024 |
| Contact name |
Trudy Oliver |
| E-mail(s) |
tgo@duke.edu, trudy.oliver@duke.edu
|
| Phone |
6174607487
|
| Organization name |
Duke University
|
| Department |
Pharmacology & Cancer Biology
|
| Lab |
theoliverlab
|
| Street address |
Duke University, Box 3813, LSRC Room C138B, 308 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL30991 |
| Series (2) |
| GSE244117 |
Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer [Spatial transcriptomics on de-identified human ONB samples] |
| GSE244123 |
Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer |
|
