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Sample GSM1972860 Query DataSets for GSM1972860
Status Public on Jul 11, 2016
Title Alpha 3
Sample type SRA
 
Source name Pancreatic Islets
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Glu-Venus
cell-type: Pancreatic alpha 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 alpha cells rep 3
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 SAMN04338146
SRA SRX1482528

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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