|
| Status |
Public on Nov 18, 2024 |
| Title |
C3-M15-4 |
| Sample type |
SRA |
| |
|
| Source name |
Th-MYCN Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Th-MYCN Tumor
treatment: Control
infiltration: T
|
| Treatment protocol |
Recruited Th-MYCN animals were treated with saline control or TEPA (400mg/kg) for three or seven days before tumor collection.
|
| Growth protocol |
Th-MYCN transgenic animals were recruited for treatment when a small tumor (3-4mm diameter) was manually palpated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A tissue microarray (TMA) was prepared using 20 Th-MYCN tumor samples (10 control, 10 TEPA-treated) in duplicate, cored at 1mm. Coring sites were chosen at random with areas exhibiting necrosis were excluded prior by an experienced histopathologist using a hematoxylin-eosin stain. The FFPE TMA block was sectioned at 4µm and transferred to a Bond Plus slide (Leica Biosystems). In brief, slides were hybridized with the GeoMx Mouse Whole Transcriptome Atlas followed by immunofluorescent staining with pan-cytokeratin (Thermo Fisher Scientific; #53-9003-82) for identification of tumor cells, smooth muscle actin (Abcam; #ab184675) for extracellular matrix, CD45 (Cell Signaling Technology; #35154) for all hematopoietic cells and DNA GeoMx Nuclear Stain (NanoString; #121303303) for cell nuclei.
The sectioned FFPE TMA block was processed by the NanoString GeoMx DSP Technology Access Program according to manufacturer's instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
TMA slides were hybridized with the GeoMx Mouse Whole Transcriptome Atlas (~18,000 targets) to generate FASTQ files.
Assembly: mm10
Supplementary files format and content: *.dcc = digital count conversion files
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc = NanoString Probe Kit Configuration file
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Nov 13, 2024 |
| Last update date |
Nov 18, 2024 |
| Contact name |
Orazio Vittorio |
| E-mail(s) |
[email protected]
|
| Organization name |
UNSW Sydney
|
| Department |
School of Biomedical Sciences, Faculty of Medicine
|
| Lab |
Metal-Targeted Therapy & Immunology (MTTI)
|
| Street address |
High St
|
| City |
Kensington |
| ZIP/Postal code |
2033 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE281844 |
Copper chelation redirects neutrophil function to enhance anti-GD2 antibody therapy in neuroblastoma [GeoMx] |
|
| Relations |
| BioSample |
SAMN44665615 |
| SRA |
SRX26678005 |
