|Public on Jul 30, 2018
|islet preparation from normo-glycemic individual 2
|islets of Langerhans
tissue compartment: islets of Langerhans
disease state: normo-glycemic
|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.
|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
|Illumina HiSeq 3000
|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").
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.
|Aug 08, 2017
|Last update date
|May 15, 2019
|Teresa L. Mastracci
|Indiana Biosciences Research Institute
|1345 W. 16th St., Suite 300,
|Functional Genomics Analysis of Islets from Recent and Longstanding T1D Reveals the Need for Distinct Approaches to Therapy