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Sample GSM3143009 Query DataSets for GSM3143009
Status Public on Jul 01, 2018
Title RealSeq_Universal miRNA Reference Kit_1 ug
Sample type SRA
 
Source name Agilent (750700)
Organism Homo sapiens
Characteristics amount: 1 ug
Extracted molecule total RNA
Extraction protocol Libraries were prepared for 1 ug of Universal miRNA Reference Kit (Agilent) with the following protocols: TruSeq Small RNA, NEXTFlex Small RNA, QIASeq miRNA, and RealSeq-AC
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model NextSeq 550
 
Description Processed data file: Raw_counts_Universal_miRNA.csv
Data processing Basecalling performed by Illumina RTA 1.18.54
Reads demultiplexed by NextSeq instrument
Reads trimmed of adapter with cutadapt with the following specifications: For TruSeq and RealSeq libraries: cutadapt -a TGGAATTCTCGGGTGCCAAGG -m 15; For NEXTFlex libraries: cutadapt -u 4 -a NNNNTGGAATTCTCGGGTGCCAAGG -m 15; For QIASeq libraries: cutadapt -a AACTGTAGGCACCATCAAT -m 15
Trimmed reads were subsampled at random to 13 million reads per library
Subsampled reads were mapped to index with the complete YM500v3 database (PMID:27899625); by using bowtie2 with the following parameters: bowtie2 -L8 --local
Raw counts of reads were obtained from sam files, by using samtools and picard-tools
Supplementary_files_format_and_content: raw counts for all small RNAs on YM500v3 database
 
Submission date May 15, 2018
Last update date Jul 01, 2018
Contact name Sergio Barberan-Soler
E-mail(s) sbarberan@somagenics.com
Phone 8314267700
Organization name Somagenics Inc
Street address 2161 Delaware Avenue
City Santa Cruz
State/province CA
ZIP/Postal code 95060
Country USA
 
Platform ID GPL21697
Series (1)
GSE107304 Increasing miRNA sequencing accuracy using an RNA circularization approach
Relations
BioSample SAMN09211360
SRA SRX4085781

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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