NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4822856 Query DataSets for GSM4822856
Status Public on Jul 07, 2022
Title Langerhans islets of NZO mice with carbohydrates
Sample type SRA
 
Source name Langerhans islets
Organism Mus musculus
Characteristics strain: New Zealand Obese (NZO/HIBomDife)
cell type: Pancreatic islets
treatment: Carbohydrate-enriched diet
gender: male
age: 18 weeks
Extracted molecule total RNA
Extraction protocol For single-cell RNA-seq, a pool of 100 islets from 3 mice per condition was dissociated using TrypLE Express (Gibco, Carlsbad, USA) for 12 min at 37 °C. Cells were then washed with PBS containing 2% FCS, filtered through a 40 µm Flowmi Cell Strainer (Bel-Art, Wayne, USA) and diluted to a final concentration of 1,000 cells/µL in PBS containing 2% FCS.
The cell suspension was immediately used for single-cell RNA-seq library preparation using the Chromium Single Cell 3ʹ Reagent Kit v3 (10X Genomics, PN-1000075, Pleasanton, USA) according to the manufacturer’s instructions.
Chromium Single Cell
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description NZO_plus_CH
Single cell gene expression of NZO+CH mice in pancreatic islets.
Data processing cellRanger 3.02
Samtools Version: 1.9 (using htslib 1.9)
Scanpy 1.4.4
Scran (version 1.16)
Scanorama (version 1.4)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.h5ad
Supplementary_files_format_and_content: *tar: Tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.
 
Submission date Oct 07, 2020
Last update date Jul 11, 2022
Contact name Pascal Gottmann
E-mail(s) pascal.gottmann@dife.de
Organization name Deutsches Institut für Ernährungsforschung
Street address Arthur-Scheunert-Allee 114-116
City Nuthetal
ZIP/Postal code 14558
Country Germany
 
Platform ID GPL24247
Series (1)
GSE159211 Single-cell RNA sequencing of pancreatic islets from obese mice with different diabetes risk reveals diabetes-susceptible β cell clusters
Relations
BioSample SAMN16392888
SRA SRX9259393

Supplementary file Size Download File type/resource
GSM4822856_filtered_feature_bc_matrix_NZO_plus_CH.tar.gz 80.8 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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