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Sample GSM7461403 Query DataSets for GSM7461403
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
 
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

Supplementary file Size Download File type/resource
GSM7461403_M28A26_aligned_fiducials.jpg.gz 1.3 Mb (ftp)(http) JPG
GSM7461403_M28A26_detected_tissue_image.jpg.gz 2.0 Mb (ftp)(http) JPG
GSM7461403_M28A26_filtered_feature_bc_matrix.h5 10.2 Mb (ftp)(http) H5
GSM7461403_M28A26_scalefactors_json.json.gz 173 b (ftp)(http) JSON
GSM7461403_M28A26_tissue_hires_image.png.gz 2.8 Mb (ftp)(http) PNG
GSM7461403_M28A26_tissue_lowres_image.png.gz 320.0 Kb (ftp)(http) PNG
GSM7461403_M28A26_tissue_positions_list.csv.gz 59.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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