|
| Status |
Public on Jul 05, 2016 |
| Title |
HP-15041 22939 |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic islets
age: adult
health: T2D
curated-cell-type: alpha
|
| Growth protocol |
islets were cultured in the standand prodo islet media (PIM-S001GMP, PIM-ABS001GMP, PIM-G001GMP) at 37oc with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Islets were dissociated to single cell by 0.05% Trypsin, 9 mins at 37oC. Cells (250-500 cells/μl) were subsequently loaded on Fluidigm C1 IFC with either 5-10 μM or 10-17 μM capture size.
Smarter-seq V2 kit was utilized for library construction per manufacturer's protocol to generate cDNA. Prepration of Illumina libraries from cDNA was done with the NexteraXT kit per Fluidigm’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Poor quality sequence was trimmed from FASTQ files.
FASTQ files were aligned to human genome hg19 and transcripts using RUM (Grant et al Bioinformatics 2011)
A best representation of each gene was selected using the highest expressing transcript, converted to RPM, and normalized to the average expression of the 10 most deeply sequenced cells.
Differential expression, where reported was performed using EdgeR or DESeq2 on raw read counts.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized expression values for RefSeq transcripts
|
| |
|
| Submission date |
Jun 08, 2016 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Jonathan Schug |
| E-mail(s) |
jschug@pennmedicine.upenn.edu
|
| Phone |
215 898 0773
|
| Organization name |
University of Pennsylvania
|
| Department |
School of Medicine
|
| Lab |
Next-Generation Sequencing Core
|
| Street address |
12-156 Smilow Ctr Trans Research
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104-5160 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE83139 |
Single cell RNA-seq of human pancreatic endocrine cells from Juvenile, adult control and type 2 diabetic donors. |
|
| Relations |
| Reanalyzed by |
GSM4812679 |
| BioSample |
SAMN05216929 |
| SRA |
SRX1832277 |
