|
| Status |
Public on Mar 19, 2020 |
| Title |
hIslets_II_A2 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic Islet cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pancreatic Islet cells
treatment: Artemether (Sigma, 10muM)
treatment time: 72hr
replicate: 2
|
| Treatment protocol |
Islets were treated with 10muM Artemether, 100 muM GABA, 10 muM FoxO inhibitor and DMSO as control for 36 and 72 hours.
|
| Growth protocol |
Human islets were extracted cadaveric donors and shipped using the Islet Integrated Distribution Program (IIDP) Mouse islets were extracted and shipped from the Collombat laboratory. Both human and mouse islets were cultured in CMRL media supplemented with 10% FBS and 1X Glutamax, and mantained in culture at 37 C in a 5% CO2 humidified atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Islet dissociation was performed by incubating the islets in accutase for 20 min at room temperature. Reaction was stopped by adding CMRL media with 10% FBS. The dissociated islets were filtered through a 40 µm filter to obtain a single-cell suspension.
Single-cell RNA-seq was performed using the Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Human pancreatic islet cells, treated with Artemether (Sigma, 10muM) for 72hr, replicate: 2
|
| Data processing |
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 2.1.0).
Sequencing data were aligned to the reference genome with Cell Ranger count and merged with Cell Ranger aggr.
Genome_build: Human: GRCh38/h38, Mouse: mm10
Supplementary_files_format_and_content: Matrices: corrected transcript per million (TPM) matrices. Data in mtx format, row names (genes), and column names (barcodes)
Supplementary_files_format_and_content: CellAnnotation_final.tsv; Annotation of cell types to barcodes
|
| |
|
| Submission date |
Dec 20, 2019 |
| Last update date |
Mar 19, 2020 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE142465 |
Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets [10X] |
| GSE147203 |
Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets |
|
| Relations |
| BioSample |
SAMN13660895 |
| SRA |
SRX7426300 |
