|
| Status |
Public on Jul 30, 2018 |
| Title |
islet preparation from normo-glycemic individual 1 |
| 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-1
|
| 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 |
SAMN07461313 |
| SRA |
SRX3070956 |
