|
Status |
Public on Jul 11, 2016 |
Title |
Delta 4 |
Sample type |
SRA |
|
|
Source name |
Pancreatic Islets
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 genotype: Sst-CreXROSA26EYFP/EYFP cell-type: Pancreatic delta cells
|
Treatment protocol |
Pancreatic alpha, beta and delta cells were isolated using a BD Influx cell sorter iinstrument based on fluorescence of Venus and EFYP
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted from FACS isolated cells using Qiagen RNasy Plus micro kit according to manufacturer's manual RNA was subjected to whole-transcriptome amplification using NuGEN RNAseq v2 System followed by fragmentation to 200bp with a Diagenode Bioruptor Pico sonicator, The resulting fragments were then used to make bar-coded libraries using NuGEN Ovation Rapid DR Multiplex System
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
pancreatic delta cells rep 4
|
Data processing |
Reads were aligned to the GRCm38/Ensembl V54 transcriptome using Tophat v2.0.8 with default parameter Raw and normalised counts using CuffLinks v2.2.1 with --max-bundle-frags 50000000 Differential gene expression was determined by EdgeR Genome_build: GRCm38 Supplementary_files_format_and_content: fastq files for raw data and FPKM values in tab-delimted txt format
|
|
|
Submission date |
Dec 15, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Brian Yee Hong Lam |
E-mail(s) |
yhbl2@cam.ac.uk
|
Organization name |
University of Cambridge
|
Department |
Metabolic Research Laboratories
|
Street address |
Box 289 Addenbookes Hospital, Hills Road
|
City |
Cambridge |
ZIP/Postal code |
CB2 0QQ |
Country |
United Kingdom |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE76017 |
Transcriptomic profiling of alpha, beta, and delta cell populations provides new insights into the role of ghrelin in the pancreas |
|
Relations |
BioSample |
SAMN04338126 |
SRA |
SRX1482538 |