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| Status |
Public on Feb 06, 2023 |
| Title |
Patient P04 Non-lesional skin sample taken at visit V06 |
| Sample type |
SRA |
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| Source name |
Healthy skin cell suspension
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| Organism |
Homo sapiens |
| Characteristics |
batch: P04_V06
patient: P04
visit: V06
tissue: Non-lesional skin
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| Treatment protocol |
NA
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| Growth protocol |
NA
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| 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 digested according to a collagenase IV skin digestion protocol (M. C. Brüggen et al, blood 2014) to generate single-cell suspensions. Single cell suspensions obtained from non-lesional and lesional skin were next incubated with commercially available DNA-labeled antibodies (TotalSeq-A, Biolegend) together with an antibody against CD45 and a cell viability dye at 4 °C for 30 min. Following incubation, cell suspensions were washed three times with PBS containing BSA. After the final wash, cell suspensions were resuspended in PBS containing BSA and a viability dye for discrimination between live and dead cells. Next, 10,000 viable CD45+ and 10,000 viable CD45- cells were sort-purified from non-lesional and lesional skin and those four cell fractions were kept separately on ice and pooled together before being processed as a single sample.
Single-cell libraries were generated using the Chromium Controller and NEXT GEM Single Cell 3′ Reagent Kit v3 or v3.1 (10x Genomics) according to the manufacturer’s protocol.
The sequencing-ready scRNA-seq 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 HiSeq 3000/4000 or the Illumina Novaseq platform (P12_V06, P13_V06) and the 75 bp paired-end configuration.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
10x genomics V3.0.2 cellranger mkfastq
10x genomics V3.0.2 cellranger count
10x genomics V3.0.2 cellranger 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: SC_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: SC_GEO_cells.csv.gz is a comma-separated text file containing single cell metadata: sample of origin, quality metrics, QC pass/fail flag
Supplementary_files_format_and_content: SC_GEO_genes.csv.gz is a comma-separated text file containing genes names and ESEMBL gene IDs
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| Submission date |
Dec 22, 2021 |
| Last update date |
Feb 06, 2023 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
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| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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| Street address |
Lazarettgasse 14
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL27644 |
| Series (2) |
| GSE192456 |
Single-cell and spatial architecture of human tissue granulomas reveals an aberrant immune-regulatory program underlying sarcoidosis [single-cell sequencing] |
| GSE192461 |
Single-cell and spatial architecture of human tissue granulomas reveals an aberrant immune-regulatory program underlying sarcoidosis |
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| Relations |
| BioSample |
SAMN24341511 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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