|
| Status |
Public on Jul 07, 2022 |
| Title |
Langerhans islets of OB mice with carbohydrates |
| Sample type |
SRA |
| |
|
| Source name |
Langerhans islets
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6.V-Lep ob/ob (OB)
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 |
OB_plus_CH
Single cell gene expression of OB+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 |
SAMN16392890 |
| SRA |
SRX9259391 |
