 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 14, 2019 |
| Title |
BL20_0 |
| Sample type |
SRA |
| |
|
| Source name |
B cell lymphoma cell line
|
| Organism |
Bos taurus |
| Characteristics |
cell line: BL20
cell type: extracellular vesicles
|
| Growth protocol |
Cells were routinely maintained in culture at 37°C in RPMI with 20% foetal calf serum (FCS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
100ml of cell culture was centrifuged at 300 x g for 10 minutes, 2000 x g for 10 minutes and 10,000 x g for 30 minutes, with cells and cell debris discarded at each stage. EV were then pelleted by ultracentrifugation using a Surespin 630 rotor (Sorvall) at 100,000 x g for 70 minutes, washed in sterile PBS and finally centrifuged at 100,000 x g for 70 minutes before resuspending in 100 ml of PBS.
RNA libraries were prepared for sequencing using standard Illumina protocols by LC Sciences (Texas)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Single end sequencing reads were cleaned with quality filter, adapter cutter, and length filter, using ACGT101_miR_v4.2g from LC Sciences.
The cleaned reads were mapped to miRBase (miRBase v21) using Bowtie v1.1.1.
The un-mapped reads were mapped to multiple databases including mRNA (NCBI Bos taurus/RNA build 09/14/2010), Rfam11, and genomic DNA (NCBI Btau 4.2), using Bowtie v1.1.1.
Novel miRNA candidates were identified from genome mapped reads based on the propensity of hairpin formation in corresponding genome positions, using ACGT101_miR_v4.2g from LC Sciences.
Data were normalized by dividing sequence counts of individual samples by corresponding normalization factors which are the median values of the ratios between specific sample counts and geometric mean counts of all samples.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Bos taurus, Btau 4.2
Supplementary_files_format_and_content: read summary and normalized data
Supplementary_files_format_and_content: Test resutls
Supplementary_files_format_and_content: final report
|
| |
|
| Submission date |
Aug 13, 2018 |
| Last update date |
May 14, 2019 |
| Contact name |
Victoria Gillan |
| E-mail(s) |
victoria.gillan@glasgow.ac.uk
|
| Organization name |
University of Glasgow
|
| Street address |
bearsden road
|
| City |
Glasgow |
| ZIP/Postal code |
g61 1qh |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19172 |
| Series (1) |
| GSE118456 |
miRNA profiling of extracellular vesicles from Theileria annulata infected B cells (TBL20) and their uninfected control counterparts (BL20) |
|
| Relations |
| BioSample |
SAMN09813021 |
| SRA |
SRX4548384 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
