|
| Status |
Public on Jun 08, 2021 |
| Title |
Bleo3 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic Islets of Langerhans_Bleo
|
| Organism |
Homo sapiens |
| Characteristics |
individual: donor 1
tissue: Pancreatic Islets of Langerhans
treatment: 50 uM bleomycin for 48 h
age: Adult
Sex: Female
disease state: Non-diabetic
|
| Treatment protocol |
After resting, islets wered culture in vehicle (DMSO) or 50 uM bleomycin in normal human islet media (RPMI1640, 10% FBS, 5.5 mM glucose, 1Xantibiotic-antimycotic) for 48 h. Islets were transferred to fresh media for 4 days of culture prior to harvest
|
| Growth protocol |
Human islets were rested in culture for 24 h prior treatments
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol-based kit and DNAse I treated
Illumina TruSeq libaries done by LC Sciences
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BleoVSVehicle_Gene_differential_expression
BleoVSVehicle_Known_lncRNA_differential_expression
BleoVSVehicle_Novel_lncRNA_differential_expression
|
| Data processing |
All bioinformatic analysis was carried out by an independent company, LC Sciences. Briefly, Cutadapt (v1.10) and perl scripts used to filter adapter contamination and undetermined bases
FastQC (v0.10.1) used to quality check sequences
BowTie2 and HISAT (v2.0.4) used to map sequences to hg38
Mapped reads assembled for each sample with StringTie (v1.3)
Comprehensive transcriptome built with perl scripts and gffcompare, StringTie and edgeR used to estimate transcript expression levels
LncRNAs identified based on filtering transcripts overlapping with known mRNAs and transcripts <200 bps. CPC and CNCI used to predict coding potential, with CPC score <-1 and CNCI score <0 removed. Remaining transcripts were considered lncRNAs. Differential expression performed using StringTie and edgeR to calculate FPKM
Genome_build: GRCh38.p12 (ENSEMBL v96) and lncRNA (v27)
Supplementary_files_format_and_content: Normalized gene and lncRNA expression levels (FPKM) from edgeR
|
| |
|
| Submission date |
Jun 07, 2021 |
| Last update date |
May 21, 2022 |
| Contact name |
Peter Thompson |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Manitoba
|
| Department |
Physiology & Pathophysiology
|
| Street address |
715 McDermot ave
|
| City |
Winnipeg |
| State/province |
MB |
| ZIP/Postal code |
R3E 3P4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE176324 |
Modeling pancreatic beta cell senescence by induction of DNA double-strand breaks |
|
| Relations |
| BioSample |
SAMN19596104 |
| SRA |
SRX11084887 |
