|
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.
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|
|
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
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|
|
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 |