|
Status |
Public on Jun 13, 2023 |
Title |
Control LKPR sample 1 (Visium) |
Sample type |
SRA |
|
|
Source name |
skin
|
Organism |
Mus musculus |
Characteristics |
tissue: skin genotype: Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ treatment: Control N/A
|
Extracted molecule |
total RNA |
Extraction protocol |
Control and NP137-treated skin tumours from LKPR mice were dissected, rinsed one part of the tumors has been kept for immunochemistry. Tumour tissues were pre-fixed in 4% PFA for 2 h at room temperature, rinsed in PBS, before to be embedded in FFPE Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to the manufacturer's recommendations
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|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
FFPE spatial transcriptome sequencing
|
Data processing |
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings Gene expression level of Refseq coding genes were quantified using Space Rangers default settings Assembly: mm10 Supplementary files format and content: filtered_feature_bc_matrix.h5 Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots Supplementary files format and content: scalefactors_json.json: scalefactors in json format Supplementary files format and content: tissue_hires_image.png: hires image of tissue Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots Library strategy: Spatial Transcriptomics
|
|
|
Submission date |
Jun 06, 2023 |
Last update date |
Jun 13, 2023 |
Contact name |
Sebastiaan Vanuytven |
E-mail(s) |
sebastiaan.vanuytven@ulb.be
|
Organization name |
Université Libre de Bruxelles
|
Street address |
Campus Erasme CP 637
|
City |
Brussels |
ZIP/Postal code |
1000 |
Country |
Belgium |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE234266 |
Pharmacological targeting Netrin-1 inhibits EMT in cancer [Visium] |
GSE234267 |
Pharmacological targeting Netrin-1 inhibits EMT in cancer |
|
Relations |
BioSample |
SAMN35648229 |
SRA |
SRX20602719 |