NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7833117 Query DataSets for GSM7833117
Status Public on Feb 06, 2024
Title Pat5
Sample type SRA
 
Source name melanoma
Organism Homo sapiens
Characteristics tissue: melanoma
treatment: anti-CTLA4 resistant
Extracted molecule total RNA
Extraction protocol Finely chopped cryopreserved material was gently thawed and dissociated using Dri Tumor & Tissue Dissociation Reagent (BD Horizon) according to manufacturer’s protocol, with digestion incubation times up to 1 hour. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotech).
The single cell suspension was processed using Chromium Single Cell 3’ Kit with Dual Index Kit TT Set A sample barcodes (10x Genomics) according to manufacturer’s recommendations. Libraries were sequenced on NovaSeq6000 (Illumina) with read length settings 28-10-10-90, according to the 10x Genomics User Guide.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing The data was processed using Cell Ranger software v6.1.2.
The h5 files were processed and merged using Seurat 4.0.1. The data were reduced to protein-coding genes. Further, translational genes (RPS/RPL in gene names), mitochondrial genes (MT- in gene names), and genes with <= 4 maximum counts were removed. Cell with less than 500 expressed genes were discarded.
Normalization of the data was performed using SCTransform, counts that were zero before normalization were returned to zero, and data was transformed by log2(data+1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file that includes raw counts for each cell
Supplementary files format and content: tab-delimited text file that includes normalized, log-transformed values for each cell
 
Submission date Oct 10, 2023
Last update date Feb 06, 2024
Contact name Martin Lauss
Organization name Lund University
Department Dept of Oncology
Street address Barngatan 2B
City Lund
ZIP/Postal code 22185
Country Sweden
 
Platform ID GPL24676
Series (2)
GSE244983 Molecular patterns of resistance to immune checkpoint blockade in melanoma [scRNA-Seq]
GSE244984 Molecular patterns of resistance to immune checkpoint blockade in melanoma

Supplementary data files not provided
Raw data not provided for this record

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