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Sample GSM3330480 Query DataSets for GSM3330480
Status Public on May 14, 2019
Title TBL20_3
Sample type SRA
 
Source name B cell lymphoma cell line
Organism Bos taurus
Characteristics cell line: TBL20
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 SAMN09813014
SRA SRX4548391

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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