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Sample GSM2735598 Query DataSets for GSM2735598
Status Public on Jul 30, 2018
Title islet preparation from normo-glycemic individual 2
Sample type SRA
 
Source name islets of Langerhans
Organism Homo sapiens
Characteristics tissue: pancreas
tissue compartment: islets of Langerhans
disease state: normo-glycemic
Growth protocol Human islets were obtained from the pancreata of deceased organ donors for research purposes. Islets were permitted to recover in culture standard human islet media (PRODO; islet media, PIM-S001GMP; human AB serum supplement, PIM-ABS001GMP; glutamine and glutathione supplement, PIM-G001GMP; Ciprofloxacin, 10 mg/mL) and then were hand-picked to separate islets from any remaining non-islet material.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated using the RNeasy Mini Extraction kit (Qiagen). Purified total RNA was eluted from the column with RNase-free water and immediately snap frozen. RNA concentration and quality was measured using a Bioanalyzer (Agilent) prior to RNA sample processing; concentrations ranged from 160 to 900 ng/uL.
paired-end RNA-seq library
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Ctrl-2
Data processing Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program Tophat.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.
 
Submission date Aug 08, 2017
Last update date May 15, 2019
Contact name Teresa L. Mastracci
E-mail(s) tmastracci@indianabiosciences.org
Organization name Indiana Biosciences Research Institute
Street address 1345 W. 16th St., Suite 300,
City Indianapolis
ZIP/Postal code 46202
Country USA
 
Platform ID GPL21290
Series (1)
GSE102371 Functional Genomics Analysis of Islets from Recent and Longstanding T1D Reveals the Need for Distinct Approaches to Therapy
Relations
BioSample SAMN07461312
SRA SRX3070957

Supplementary file Size Download File type/resource
GSM2735598_Ctrl-2.gtf.gz 4.0 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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