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Sample GSM2123266 Query DataSets for GSM2123266
Status Public on Aug 01, 2016
Title TRIzol+MS2_unpooled 2
Sample type SRA
 
Source name TRIzol+MS2_unpooled_serum
Organism Homo sapiens
Characteristics tissue: Serum
sample type: Orphan samples
sample type: DoD Serum Repository
sample type: small RNA
sample type: unpooled serum samples
rna extraction method: TRIzol+MS2
Extracted molecule total RNA
Extraction protocol Different extraction procedures such as TRIzol with and without carrier glycogen/yeast tRNA/bacteriophage MS2), miRNAeasy ,mirVANA and TRIzol with exosome precipitation using exoquick buffer.
Illumina Trueseq small RNA kit
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiScanSQ
 
Data processing Basecalls performed using CASAVA version 1.8.2
Reads were processed further for quality assessment, quality filtering, and adaptor trimming, and quality filtered again using a Phred quality score threshold of 20
The ligated adaptor sequences were trimmed, leaving a minimum overlap of five bases while allowing an error rate of 0.1 using CutAdapt 1.2.1
Using the short read aligner Bowtie 1.0.0 [27], filtered sequence reads were aligned to the Human reference genome assembly humanv37 from Ensembl and the best hits to the genome were identified using BEDtools 2.17
Small RNA species were annotated by mapping with the reference gene feature annotation table from the Ensembl database
Quantification/enrichment reads for miRNAs were first aligned to the Rfam RNA families database to filter other small RNA species, and then reads were mapped for small RNA annotation against reference.mature/precursor hg19_mature RNA sequences from the miRBase (miRbase 19)database .The miRNA read count matrix for each sample was generated using open source tools Picard 1.84
Genome_build: mirBASE19
Supplementary_files_format_and_content: miRNA count file
 
Submission date Apr 14, 2016
Last update date May 15, 2019
Contact name Aarti Gautam
E-mail(s) aarti.gautam.civ@health.mil
Phone 301-619-7683
Organization name WRAIR
Department Medical Readiness Systems Biology
Street address 503 Robert Grant Avenue
City Silver Spring
State/province MD
ZIP/Postal code 20910
Country USA
 
Platform ID GPL15456
Series (1)
GSE80274 Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods
Relations
BioSample SAMN04853054
SRA SRX1704746

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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