|
| Status |
Public on Jun 09, 2023 |
| Title |
Mouse #19331 spatial transcriptomics |
| Sample type |
SRA |
| |
|
| Source name |
Spatial transcriptomics of melanoma at 35 days post induction
|
| Organism |
Mus musculus |
| Characteristics |
genotype: dKO
Sex: F
tissue: Melanoma tissue section
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was prepared according to 10X Genomics Visium V1 Slide - 3' Spatial guidelines. Resected BRAFV600E/PTEN-deficient melanomas were first frozen in a bath of isopentane and liquid nitrogen, stored at –80°C in a sealed container, then embedded in OCT compound. Tissue was sectioned at temperatures of -20°C for the cryostat chamber and -10°C for the specimen head, at 10 μm thickness. An optimal permeabilization time of 18 min was determined using the Visium Spatial Tissue Optimization Kit (10x Genomics).
Libraries were constructed according to the manufacturer’s guidelines for Visium Spatial (10X Genomics) followed by sequencing on a S1 NovaSeq chip (Illumina Inc.). Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent) were used for quality check of cDNA.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
clustered_spatial_object.RData
annotated_spatial_object.RData
|
| Data processing |
library strategy: Spatial transcriptomics
Sequencing data was mapped using spaceranger v2.0.0 using the mm10‑2020‑A transcriptome (10X Genomics) to generate spatial gene expression matrices.
Data was further processed according to the Seurat spatial vignette (https://satijalab.org/seurat/articles/spatial_vignette.html). We integrated data normalized with SCTransform v2 across the two ST samples.
Clusters were determined using a variety of resolutions and annotated using top cluster-specific genes conserved between WT and dKO cells.
Assembly: mm10-2020-A transcriptome
Supplementary files format and content: One h5 file including filtered features, one file for scale factors, one high resolution tissue image and a list of tissue positions used as input for Seurat, for each sample. One RData Seurat object containing the integrated cells across 2 samples, final clustering up to removal of clusters representing low-quality cells. One RData Seurat object containing the annotated clusters retained for further analysis.
|
| |
|
| Submission date |
Apr 12, 2023 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Dan Filipescu |
| E-mail(s) |
dan.filipescu@mssm.edu
|
| Phone |
2128249265
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Oncological Sciences
|
| Lab |
Emily Bernstein
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE200751 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts. |
| GSE229532 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts [spatial transcriptomics] |
|
| Relations |
| SRA |
SRX19947764 |
| BioSample |
SAMN34159468 |
