|
| Status |
Public on Dec 19, 2015 |
| Title |
cardiac fibroblast-derived exosomes sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
cardiac fibroblast-derived exosomes
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: wistar
tissue: heart
rna source: cardiac fibroblast-derived exosomes
developmental stage: P1-P2
|
| Treatment protocol |
For exosome purification, neonatal rat cardiac fibroblasts were cultured in DMEM + 1% exosome-depleted FBS for 48h. Conditioned medium was collected and exosomes were purified by several centrifugation and filtration steps, following ultracentrifugation. Afterwards total RNA from cardiac fibroblasts and exosomes was isolated for miRNA sequencing.
|
| Growth protocol |
Neonatal rat cardiac fibroblasts were isolated from newborn rats by enzymatic digestion and were cultured in DMEM (PAA) supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and exosomes were collected from fibroblast conditioned medium and RNA was isolated using Trizol reagent.
Small RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed using cutadapt version 1.2.1
mature miRNA sequences for rattus norvegicus were downloaded from miRBase version 20
trimmed reads were mapped using NCBI blast version 2.2.28+ against the miRNA reference database created from mature miRNA
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized read counts and differential expression analysis from DESeq. In the file Differential_expression_DESeq.txt, baseMeanA represents Cardiac fibroblast and baseMeanB represents Cardiac fibroblast exosome.
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Claudia Bang |
| E-mail(s) |
[email protected]
|
| Phone |
+ 49 511 5325276
|
| Organization name |
Medical School Hannover
|
| Street address |
Carl-Neuberg-Straße 1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE76175 |
microRNA sequencing in rat cardiac fibroblasts and fibroblast-derived exosomes |
|
| Relations |
| BioSample |
SAMN04351361 |
| SRA |
SRX1492111 |
