|
| Status |
Public on Jul 25, 2019 |
| Title |
HIP30 |
| Sample type |
SRA |
| |
|
| Source name |
HIP30
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
genotype: transgenic (HIAPP-expressing, or HIP)
tissue: pancreatic duct gland
|
| Treatment protocol |
The PDG compartment was identified morphologically and cut into 0.5 ml tube cap filled with 10 µl of extraction buffer and 0.5 µl RNase inhibitor. To avoid RNA degradation, slides were processed one at a time, and staining and dissection from each slide was finished within 20 min. The LCM procedure was performed using a Leica LMD7000 Laser Microdissection system
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the PicoPure® RNA Isolation Kit, KIT0204
Libraries prepared using the Nugen Ultra Low Mass RNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA derived from the pancreatic duct gland compartment in HIAPP-expressing transgenic animals (HIP)
|
| Data processing |
Aligned to rn5 using STAR spliced read aligner
Count read using HT-seq and using rn5 RefSeq as reference
Genes with count 0 across samples were removed. Normalization (TMM), quantitation (logCPM) and differential expression analysis using edgeR and limma voom.
Genome_build: rn5
Supplementary_files_format_and_content: logCPM values
|
| |
|
| Submission date |
Jul 25, 2018 |
| Last update date |
Jul 26, 2019 |
| Contact name |
Giovanni Coppola |
| E-mail(s) |
gcoppola@ucla.edu
|
| Phone |
310-794-4172
|
| Organization name |
UCLA
|
| Department |
Psychiatry and Neurology
|
| Lab |
Neurogenetics
|
| Street address |
1524 Gonda, 695 Charles Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE117679 |
In the Setting of Beta Cell Stress, the Pancreatic Duct Gland Transcriptome shows Characteristics of an Activated Regenerative Response |
|
| Relations |
| BioSample |
SAMN09716663 |
| SRA |
SRX4459967 |
