|
| Status |
Public on Feb 23, 2016 |
| Title |
Islet_NOD.Rag-/-.insHEL_#3 |
| Sample type |
SRA |
| |
|
| Source name |
isolated pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOD/LtJ;BR-H2k.129S7(B6)-Ragtm1Mom.B6-Tg(ILK3mHEL)3Ccg
gender: male
age: 11 weeks
tissue: pancreatic islet
haplotype: MHC k
genotype/variation: Rag-/-.insHEL
phenotype: normoglycemia
total islet number: 77
|
| Treatment protocol |
Pancreata were digested by 0.8mg/mL collagenase NB 8 (Serva/Bio Connect) at 37 degree for 15 minutes. Digested pancreatic tissue were washed once with 20mL HBSS and re-suspend in 28% Dextron T70 solution. Islets were purified by Dextron T70 density gradient centrifugation (25.7%, 22.4%, 12.3%) and picked out under microscope. α-Amanitin(2μg/mL, Sigma) and Actinomycin D (5μg/mL, Sigma) were added to collagens NB 8 and HBSS solution used for isolation. Picked islets were washed once with 1mL HBSS.
|
| Growth protocol |
Islets were suspended with 1mL Trizol (Invitrogen) and freezed in -20 degree immediately after isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini kit (Qiangen) following the provided protocol.
RNA libraries were prepared for sequencing using Illumina Truseq Stranded mRNA library prep (versie 15031047_D)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample015
|
| Data processing |
Sequenced reads were trimmed for quality (Q > 20, fastx toolkit), adaptor sequence (cutadapt), and filtered for low-quality sequence, low-complexity and illumina internal control phiX. Then mapped to the mouse GRCm38.73 whole genome (downloaded from ensembl) using tophat v2.0.8b with parameters --library-type fr-unstranded --min-intron-length 50 --max-intron-length 500000 --no-coverage-search --no-mixed --read-realign-edit-dist 3
The number of reads mapping to each Ensembl gene was counted with htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count; parameters: union and reverse stranded). Non-normalized counts used for a DESeq analysis.
Genome_build: GRCm38.73
Supplementary_files_format_and_content: htseq-count-table.txt contains non-normalized read counts assigned to genes.
|
| |
|
| Submission date |
Apr 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE56507 |
Comparative assessment of the transcriptome of pancreatic islets from Non-Obese Diabetic mice in the absence of immune infiltrate |
|
| Relations |
| BioSample |
SAMN02717036 |
| SRA |
SRX510965 |
