|
| Status |
Public on Jan 16, 2024 |
| Title |
Patient A2 active psoriatic arthritis synovial spatial transcriptomics |
| Sample type |
SRA |
| |
|
| Source name |
synovial joint
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: synovial joint
disease: psoriatic arthritis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Unfixed human synovial biopsies were snap frozen in OCT Tissue TEK (Sacura). 10 µm thin sections were cut on a Cryotome FSE (Thermo Fisher)
Spatial transcriptomes was generated according to the Visium Spatial Gene Expression Kit (v1 chemistry, 10x Genomics). An optimisation slide was run for optimal permeabilisation conditions. 6 min was found to be optimal. Spatial transcriptomes were prepared according to the Visisum protocol CG000239 Rev B). Libraries were sequenced as PE150 by Illumina sequencing to >80% saturation by the external provider Novogene.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were mapped to the human genome GRCh38 (GENCODE v32/Ensembl 98) using 10x Genomics’ space ranger pipeline (1.2.1) with default settings and manual correction of spots under tissue using Loupe Cell Browser (5.0.1).
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: tissue H&E image files (low resolution and high resolution)
Supplementary files format and content: Comma separated tissue positions file
Supplementary files format and content: scale factor json file
Library strategy: Spatial transcriptomics
|
| |
|
| Submission date |
Apr 04, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Hashem Mohammadian |
| Organization name |
University of Erlangen-Nürnberg
|
| Department |
Department of Medicine 3 - Rheumatology and Immunology
|
| Street address |
Ulmenweg 18
|
| City |
Erlangen |
| ZIP/Postal code |
91054 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE228972 |
Molecular reframing of fibroblasts during resolution of arthritis [Visium] |
| GSE228982 |
Molecular reframing of fibroblasts during resolution of arthritis |
|
| Relations |
| BioSample |
SAMN34082554 |
| SRA |
SRX19868410 |
