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| Status |
Public on Jul 17, 2024 |
| Title |
DMBA/TPA-induced skin tumor Visium Spatial Transcriptomics, replicate 4 (C1_231204) |
| Sample type |
SRA |
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| Source name |
mouse epidermis
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| Organism |
Mus musculus |
| Characteristics |
tissue: mouse epidermis
treatment: DMBA/TPA carcinogenesis
strain: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J
age: 144 days post natal
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| Treatment protocol |
DMBA/TPA chemical carcinogenesis: Two-stage cutaneous chemical carcinogenesis was performed as previously described by Filler et al. (2007). In brief: the back of 6-8 week old animals were shaved with electric hair clippers and treated once with 400 nmol 7,12-dimethylbenz[a]anthracene (DMBA)(Sigma-Aldrich D3254) per 100 µl (dissolved in acetone) application as an initiator mutagen. After a two-week rest period, 40 nmol 2-o-tetradecanoylphorbol-13-acetate (TPA)(Sigma-Aldrich 79346) dissolved in 100 µl 100% Ethanol was applied twice a week. Tumor formations were monitored regularly by visual inspection and mice were euthanized after 12 weeks of treatment or when tumors reached a cumulative length of 2cm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
A microarray of fresh-frozen DMBA/TPA-induced squamous cell carcinoma samples, surgically removed from mouse back skin, was cryo-sectioned with a 10µm thickness (Leica, CM3050S) and placed on the capture area of a spatial gene expression slide (10x Genomics, 1000188), resulting in 4 different tumors on a single capture area. Samples were stored in -80°C before processing.
The workflow of Mirzazadeh et al. (2023) for RNA-Rescue Spatial Transcriptomics (RRST) was followed to overcome low RNA integrity number (RIN) score. The samples were fixed with 4% PFA and hematoxylin and eosin (H&E) staining was performed. The spatial libraries were then generated from the probe hybridization step (10x Genomics, 1000365) according to Visium Spatial Gene Expression Reagent Kits for FFPE (10x Genomics, User Guide CG000407 Rev D, 1000361). The resulting libraries were sequenced by the Genomics Facility Basel. The sequencing was performed in a paired-end manner with dual indexing (10x Genomics, 1000251) on a NovaSeq 6000 (Illumina) with a SP flow cell (51bp read length).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
library strategy: Spatial Transcriptomics
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. FASTQ files were processed using Space Ranger software (version 2.0.1, 10x Genomics). Reads were aligned with the ‘spaceranger count’ pipeline to the pre-built mouse reference genome provided by 10x Genomics version 2020-A (comprising the STAR-indexed mm10 mouse genome and the GTF gene annotation from GENCODE version M23 (Ensembl 98)), and the probe set reference CSV file (Visium Mouse Transcriptome Probe Set v1.0) was provided for filtering of valid genes. The resulting filtered count matrix of features (i.e. genes) per spot barcodes were employed for the downstream analysis.
genome build/assembly: mm10
processed data files format and content: *_barcodes.tsv.gz: list of spatial barcodes; *_features.tsv.gz: list of gene IDs; *_matrix.mtx.gz: gene-barcode expression count data in Matrix Market Exchange Format; *_aligned_fiducials.jpg: aligned fiducials of the tissue image; *_detected_tissue_image.jpg: image of tissue and spots; *_scalefactors_json.json: scalefactors in JSON format; *_tissue_hires_image.png: hi-res image of tissue; *_tissue_lowres_image.png: low-res image of tissue; *_tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Assembly: mm10
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| Submission date |
May 20, 2024 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Simona Baghai Sain |
| Organization name |
ETH Zurich
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| Department |
Department of Biosystems Science and Engineering
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| Street address |
Schanzenstrasse 44
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| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE235325 |
In vivo single-cell CRISPR uncovers distinct TNF-α programs in tumor evolution |
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| Relations |
| BioSample |
SAMN41456109 |
| SRA |
SRX24606808 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8279998_C1_mouse_tumor_skin_231204_aligned_fiducials.jpg.gz |
1.6 Mb |
(ftp)(http) |
JPG |
| GSM8279998_C1_mouse_tumor_skin_231204_barcodes.tsv.gz |
10.4 Kb |
(ftp)(http) |
TSV |
| GSM8279998_C1_mouse_tumor_skin_231204_detected_tissue_image.jpg.gz |
771.6 Kb |
(ftp)(http) |
JPG |
| GSM8279998_C1_mouse_tumor_skin_231204_features.tsv.gz |
164.2 Kb |
(ftp)(http) |
TSV |
| GSM8279998_C1_mouse_tumor_skin_231204_matrix.mtx.gz |
1.0 Mb |
(ftp)(http) |
MTX |
| GSM8279998_C1_mouse_tumor_skin_231204_scalefactors_json.json.gz |
192 b |
(ftp)(http) |
JSON |
| GSM8279998_C1_mouse_tumor_skin_231204_spatial_enrichment.csv.gz |
679.9 Kb |
(ftp)(http) |
CSV |
| GSM8279998_C1_mouse_tumor_skin_231204_tissue_hires_image.png.gz |
5.3 Mb |
(ftp)(http) |
PNG |
| GSM8279998_C1_mouse_tumor_skin_231204_tissue_lowres_image.png.gz |
521.6 Kb |
(ftp)(http) |
PNG |
| GSM8279998_C1_mouse_tumor_skin_231204_tissue_positions.csv.gz |
68.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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