NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5747449 Query DataSets for GSM5747449
Status Public on Feb 06, 2023
Title Cryosection nr. 1 from patient P07. Granuloma biopsy taken at visit V06
Sample type SRA
 
Source name Biopsy from cutaneous granuloma
Organism Homo sapiens
Characteristics batch: P07_V06
patient: P07
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 SAMN24341530

Supplementary data files not provided
Processed data are available on Series record
Raw data not provided for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap