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Sample GSM3122081 Query DataSets for GSM3122081
Status Public on Oct 30, 2018
Title hPSC medium
Sample type SRA
 
Source name Pluripotent stem cell culture medium
Organism other sequences
Characteristics sex/karyotype: n/a
passage: n/a
source/details: n/a
Extracted molecule total RNA
Extraction protocol EVs were isolated from 3 ml conditioned cell culture media using miRCURY™ Exosome Isolation kit (Exiqon A/S) followed by RNA isolation using miRCURY™ RNA Isolation Kits - Cell & Plant (Exiqon A/S).
The library preparation was done using the NEBNext® Small RNA Library preparation kit (New England Biolabs). A total of 6 μl isolated RNA was converted into microRNA NGS libraries. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent). Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The pool was then size selected using the LabChip XT (PerkinElmer) aiming to select the fraction with the size corresponding to microRNA libraries (~ 145 nt). The library pool were then sequenced on a NextSeq 500 sequencing instrument according to the manufacturer instructions.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Data processing Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.).
Reads were mapped using Bowtie 2 software according to the Exiqon NGS Service microRNA/smallRNA pipeline. First, reads aligned to spike-ins or abundant sequences were discarded. Second, reads were aligned to miRBase 20. Third, unaligned reads were aligned to miRNA and smRNA loci in GRCh37 reference genome. Reads aligned to miRNA loci were combined with reads aligned to miRBase.
Genome_build: GRCh37
Supplementary_files_format_and_content: mirna_raw_counts.txt: tab-delimited text file including miRNA raw counts for all samples, smrna_raw_counts.txt: tab-delimited text file including other smRNA raw counts for all samples
 
Submission date Apr 30, 2018
Last update date Oct 30, 2018
Contact name Sippy Kaur
E-mail(s) sippy.kaur@helsinki.fi
Organization name University of Helsinki
Department Oral and Maxillofacial Diseases
Street address PO Box 63
City Helsinki
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL24755
Series (1)
GSE113868 Small RNA non-coding landscape of extracellular vesicles from human stem cells
Relations
BioSample SAMN09002961
SRA SRX4014260

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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