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Sample GSM7807489 Query DataSets for GSM7807489
Status Public on May 15, 2024
Title 3.2_reg1_CD45-Ki-67
Sample type RNA
 
Source name olfactory neuroblastoma
Organism Homo sapiens
Characteristics tissue: olfactory neuroblastoma
grade: II
Stage: D
location: cervical LN
Sex: M
age: 44
Extracted molecule total RNA
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

Data table header descriptions
ID_REF
VALUE Matrix table contains, raw, unfiltered gene count matrices from all ROI segments profiled.

Data table
ID_REF VALUE
A2M 4
NAT2 0
ACADM 4
ACADS 0
ACAT1 1
ACVRL1 0
PSEN1 1
ADA 2
SGCA 3
ADRB2 3
ADRB3 3
AGL 4
AGXT 1
ABCD1 0
ALDOB 4
AMPD1 0
APC 3
APOA1 3
APOC3 1
APOE 3

Total number of rows: 18676

Table truncated, full table size 153 Kbytes.




Supplementary file Size Download File type/resource
GSM7807489_DSP-1001660018527-A-D10.dcc.gz 45.1 Kb (ftp)(http) DCC

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