|
| Status |
Public on Jul 17, 2014 |
| Title |
81 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic islets
age: 69
bmi: 24.5
gender: Male
year of birth: 1942
hba1c: 5.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreatic islets were isolated according to the isolation protocol described from Nordic Islet Transplantation Programme (http://www.nordicislets.org). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Paired-end 101bp length output reads were aligned to the human reference genome (UCSC hg19) with TopHat v.2.0.2 (PMID: 19289445) using Bowtie v.0.12.8 (PMID: 19261174). The TopHat parameters explicitly used are tophat -p 30 -G genes.gtf --library-type fr-unstranded -r 100 -F 0.05 --microexon-search.
The annotated RefSeq GTF transcript and fasta genome files were from UCSC and were downloaded from http://cufflinks.cbcb.umd.edu/igenomes.html. Gene expression was measured as the normalized sum of expression of all its exons. The dexseq_count python script (PMID: 22722343) was used by counting uniquely mapped reads in each exon.
Gene and exon expression normalizations were then performed using the TMM method (PMID: 20196867), and further normalization was applied by adjusting the expression to gene or exon length respectively.
In addition, only the genes and exons that had reads mapped to them in at least 5% of the samples were kept.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TMM gene and exon values normalized for each Sample (and also normalized by gene and exon length respectively). The processed files also include the genomic coordinates of the genes and exons annotated
|
| |
|
| Submission date |
Aug 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joao Fadista |
| E-mail(s) |
joao.fadista@med.lu.se
|
| Organization name |
Lund University Diabetes Centre
|
| Street address |
Jan Waldenströms gata 35
|
| City |
Malmö |
| ZIP/Postal code |
205 02 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE50244 |
Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [RNA-seq] |
| GSE50398 |
Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism |
|
| Relations |
| BioSample |
SAMN02335306 |
| SRA |
SRX340198 |
