|
| Status |
Public on Oct 07, 2024 |
| Title |
KneeOA_ObeseBMI14 (ST) |
| Sample type |
SRA |
| |
|
| Source name |
Infrapatellar Fat Pad
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Infrapatellar Fat Pad
condition: OA
procedure: Total Knee Replacement
age: 57
Sex: female
bmi: 39.2
bmi category: Obese
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh frozen human fat pad samples were embedded in Optimal Cutting Temperature (OCT) medium and frozen in liquid nitrogen. The frozen tissue block was cut into 10 μM sections in a cryostat. RNA was isolated using the Qiagen RNeasy Mini kit per manufacturer’s recommendations. RNA quality control was performed with the Agilent Bioanalyzer using the RNA 6000 Nano Kit.
Spatial sequencing libraries were constructed using the 10X Genomics Visium CytAssist Spatial Gene Expression Reagent Kits. Library quality was assessed on a high sensitivity DNA chip on the Bioanalyzer. Sequencing libraries were volumetrically pooled and sequenced on an Illumina NovaSeq sequencer for 150 paired end read-cycles at the Princess Margaret Genomics Cancer Centre (Toronto, ON, Canada).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
fresh frozen spatial transcriptomics sequencing
|
| Data processing |
Raw sequencing data were processed using 10X Genomics Space Ranger pipeline to make FASTQ files
Reads were aligned to human genome and transcriptome (vGrCh38) to gene expression count using Space Ranger's default parameters.
Normalization and deconvolution using snRNA-seq data was performed with help of Seurat (v5.0.1) R package and integration of all sequenced samples was performed using Harmony (v0.1.1) R package.
Assembly: GrCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: matrix of gene expression counts
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image: 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: hi-res 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 coordinates specifying spots
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Jan 13, 2024 |
| Last update date |
Oct 07, 2024 |
| Contact name |
Mohit Kapoor |
| E-mail(s) |
mohit.kapoor@uhnresearch.ca
|
| Organization name |
Schroeder Arthritis Institute
|
| Street address |
60 Leonard Ave
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 0S8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE253199 |
Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis [Spatial Transcriptomics] |
| GSE253200 |
Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis |
|
| Relations |
| BioSample |
SAMN39432636 |
| SRA |
SRX23206497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8016283_KneeOA_ObeseBMI14_aligned_fiducials.jpg.gz |
2.4 Mb |
(ftp)(http) |
JPG |
| GSM8016283_KneeOA_ObeseBMI14_aligned_tissue_image.jpg.gz |
1.3 Mb |
(ftp)(http) |
JPG |
| GSM8016283_KneeOA_ObeseBMI14_barcodes.tsv.gz |
16.5 Kb |
(ftp)(http) |
TSV |
| GSM8016283_KneeOA_ObeseBMI14_cytassist_image.tiff.gz |
16.3 Mb |
(ftp)(http) |
TIFF |
| GSM8016283_KneeOA_ObeseBMI14_detected_tissue_image.jpg.gz |
1.2 Mb |
(ftp)(http) |
JPG |
| GSM8016283_KneeOA_ObeseBMI14_features.tsv.gz |
152.8 Kb |
(ftp)(http) |
TSV |
| GSM8016283_KneeOA_ObeseBMI14_matrix.mtx.gz |
11.9 Mb |
(ftp)(http) |
MTX |
| GSM8016283_KneeOA_ObeseBMI14_scalefactors_json.json.gz |
199 b |
(ftp)(http) |
JSON |
| GSM8016283_KneeOA_ObeseBMI14_spatial_enrichment.csv.gz |
708.4 Kb |
(ftp)(http) |
CSV |
| GSM8016283_KneeOA_ObeseBMI14_tissue_hires_image.png.gz |
3.5 Mb |
(ftp)(http) |
PNG |
| GSM8016283_KneeOA_ObeseBMI14_tissue_lowres_image.png.gz |
369.2 Kb |
(ftp)(http) |
PNG |
| GSM8016283_KneeOA_ObeseBMI14_tissue_positions.csv.gz |
69.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
