|
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |