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Sample GSM7727539 Query DataSets for GSM7727539
Status Public on Aug 29, 2023
Title Sample1
Sample type SRA
 
Source name Carotid plaque tissue
Organism Homo sapiens
Characteristics tissue: Carotid plaque tissue
cell type: Mixed
treatment: No treatment
Extracted molecule total RNA
Extraction protocol A 5μm tissue section from each carotid plaque sample was placed onto one capture area of a Visium Spatial Gene Expression slide. Two samples were selected form Asymptomatic male patients for spatial RNA-seq.
Visium for formalin-fixed paraffin-embedded (FFPE) spatial gene expression slide and reagent kit was used according to manufacturer instructions (PN: 1000338; 10X Genomics).
OTHER: Spatial Transcriptomics
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model NextSeq 2000
 
Description Fresh frozen spatial RNA-sequencing
Data processing Raw sequencing data were processed with the 10X Genomics Space Ranger pipeline to generate fastq files.
The FASTQ files and the manually aligned histology images were analyzed with Space Ranger 1.3.1 and the human probeset provided by 10X genomics (Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A).
Visualization of spatial cluster output from Space Ranger as well as differential gene expression analysis to determine cluster-specific up- or downregulated genes was performed on Loupe Browser 6.0.0 (10X Genomics).
Assembly: mm10
Supplementary files format and content: barcodes.tsv list of spatial barcodes
Supplementary files format and content: features.tsv list of Gene IDs
Supplementary files format and content: matrix.mtx gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg aligned figucials of the tissue image
Supplementary files format and content: scalefactors_json.json scale factors in json format
Supplementary files format and content: detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: tissue_hires_image.png high res image of tissue
Supplementary files format and content: tissue_low_image.png low res image of tissue
Supplementary files format and content: tissue_posotions_list.csv list of spatial barcodes and thecoordinates specifying spots
 
Submission date Aug 21, 2023
Last update date Jan 20, 2024
Contact name Konstantinos Theofilatos
E-mail(s) konstantinos.theofilatos@kcl.ac.uk
Organization name King's CollegeLondon
Street address 125 Coldharbour Lane
City London
ZIP/Postal code SE5 9NU
Country United Kingdom
 
Platform ID GPL30173
Series (1)
GSE241346 A Proteomic Atlas of Atherosclerosis: The Contribution of Proteoglycans to Sex Differences, Plaque Phenotypes and Outcomes
Relations
BioSample SAMN37099266
SRA SRX21439576

Supplementary file Size Download File type/resource
GSM7727539_sample1_aligned_fiducials.jpg.gz 754.2 Kb (ftp)(http) JPG
GSM7727539_sample1_barcodes.tsv.gz 25.1 Kb (ftp)(http) TSV
GSM7727539_sample1_detected_tissue_image.jpg.gz 642.5 Kb (ftp)(http) JPG
GSM7727539_sample1_features.tsv.gz 290.1 Kb (ftp)(http) TSV
GSM7727539_sample1_matrix.mtx.gz 3.5 Mb (ftp)(http) MTX
GSM7727539_sample1_scalefactors_json.json.gz 156 b (ftp)(http) JSON
GSM7727539_sample1_tissue_hires_image.png.gz 997.6 Kb (ftp)(http) PNG
GSM7727539_sample1_tissue_lowres_image.png.gz 108.5 Kb (ftp)(http) PNG
GSM7727539_sample1_tissue_positions_list.csv.gz 57.9 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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