|
| Status |
Public on Feb 06, 2023 |
| Title |
Cryosection nr. 1 from patient P06. Granuloma biopsy taken at visit V06 |
| Sample type |
SRA |
| |
|
| Source name |
Biopsy from cutaneous granuloma
|
| Organism |
Homo sapiens |
| Characteristics |
batch: P06_V06
patient: P06
visit: V06
section nr.: 1
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
6mm punch-biopsies were taken from affected skin as well as skin presenting no signs of inflammation before treatment. Sarcoidosis has been histologically and clinically confirmed by trained dermatologists. Fresh biopsies were embedded in optimal cutting temperature (OCT) compound and stored as sectioning blocks at -80 °C until further processing. Before undertaking the full protocol, a tissue optimization experiment (10x Genomics, Visium Spatial Tissue Optimization) was performed using cryosections of patient skin biopsies with imaging of fluorescence signal identifying 18 minutes as optimum permeabilization time.
Spatial transcriptomic libraries were generated using the Visium Spatial gene expression reagent kit (10x Genomics) according to the manufacturer’s protocol.
The sequencing-ready spatial transcriptomics libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina Novaseq platform and the 75 bp paired-end configuration.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
10x genomics V3.0.2 cellranger mkfastq
10x genomics V1.2.0 spaceranger count
10x genomics V1.2.0 spaceranger aggr
custom Python notebook used to convert the matrix from cellranger into csv format (without additional processing), generate QC metrics and metadata files (see project repository)
Genome_build: GRCh38
Supplementary_files_format_and_content: ST_GEO_raw_counts.csv.gz is a comma-separated, gzipped file containing a Cells (rows) x Genes (columns) raw counts matrix (includes header and row names)
Supplementary_files_format_and_content: ST_GEO_spots.csv.gz is a comma-separated text file containing single spot metadata: sample of origin, QC metrics and spot location
Supplementary_files_format_and_content: ST_GEO_genes.csv.gz is a comma-separated text file containing genes names and ESEMBL gene IDs
|
| |
|
| Submission date |
Dec 22, 2021 |
| Last update date |
Feb 06, 2023 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL27644 |
| Series (2) |
| GSE192460 |
Single-cell and spatial architecture of human tissue granulomas reveals an aberrant immune-regulatory program underlying sarcoidosis [spatial transcriptomics data] |
| GSE192461 |
Single-cell and spatial architecture of human tissue granulomas reveals an aberrant immune-regulatory program underlying sarcoidosis |
|
| Relations |
| BioSample |
SAMN24341529 |
