NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7779047 Query DataSets for GSM7779047
Status Public on Jan 11, 2024
Title Spinal_snRNA-seq_5
Sample type SRA
 
Source name Spinal cord
Organism Homo sapiens
Characteristics tissue: Spinal cord
age: 49 years old
Extracted molecule polyA RNA
Extraction protocol Nuclei were isolated using a Nucleus Isolation Kit (catalogue no. 52009-10, SHBIO, China) according to the manufacturer’s instructions. Nuclei suspension was loaded onto a Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEM) using single cell 3' Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074) according to the manufacturer’s protocols.
The 10x snRNA-seq library was established using Single Cell 3’ Library and Gel Bead Kit V3.1, according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 220719B_spinal_5L
Data processing Basecalls performed using bcl2fastq.gz tools
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v5.0.1), including demultiplexing the fastq.gz reads, aligning them to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and counting the unique molecular identifier (UMI) (by using ‘cellranger count’ function).
Assembly: GRCh38
Supplementary files format and content: Tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices
 
Submission date Sep 13, 2023
Last update date Jan 11, 2024
Contact name Donghang Zhang
Organization name West China Hospital of Sichuan University
Street address No.37, guoxue lane, wuhou district, chengdu city, sichuan province
City Chengdu
State/province Sichuan
ZIP/Postal code 610041
Country China
 
Platform ID GPL24676
Series (2)
GSE243076 Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [Spinal snRNA-seq]
GSE243077 Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord
Relations
BioSample SAMN37385914
SRA SRX21771590

Supplementary file Size Download File type/resource
GSM7779047_Spinal_5_filtered_feature_bc_matrix.tar.gz 50.9 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

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