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| Status |
Public on Jan 29, 2016 |
| Title |
Sample_1S5 |
| Sample type |
SRA |
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| Source name |
plasma microvesicles
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| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
age (years): 54
disease status: Cancer
disease type: Colorectal Cancer
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| Extracted molecule |
total RNA |
| Extraction protocol |
microvesicles were isolated from 250 μL of plasma using the ExoQuick exosome precipitation solution (System Biosciences, Mountain View, CA, USA). Microvesicle RNA was prepared using a miRNeasy Micro Kit (QIAGEN, Valencia, CA, USA)
Libraries were prepared according to NEBNext multiplex small RNA library preparation kit (NEB, New England Biolab, Ipswich, MA, USA). For detail, see Huang X at al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics, 2013; 14:319. PMCID: PMC3653748
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
exRNA seq
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and then mapped to different RNA species using bowtie v1.1.1 with parameters -l 18, -v 1, -m 2, and --norc --best --strata
An iterative alignment strategy was ued: unmapped sequences from the previous alignment were used for the mapping of the next RNA reference species. The sequential alignment followed the order of mature miRNA, precursor miRNA, piwiRNA, siRNA, lncRNA, mRNA, pseudo genes, antisense RNA, rRNA, snRNA, snoRNA, misc-RNA, other transcribed RNA, FLJ human cDNA, and predicted RNA.
Reads per Megabase of library size (RPM) were calculated.
For detail, please see Yuan T et al. eRNA: A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. BMC Genomics, 2014, 15:176. PMCID: PMC4029068
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample
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| Submission date |
Jul 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Liang Wang |
| E-mail(s) |
liwang@mcw.edu
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| Phone |
414-955-2574
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| Organization name |
Medical College of Wisconsin
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| Department |
Pathology
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| Street address |
8701 Watertown Plank Rd.
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| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53226 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE71008 |
Plasma extracellular RNA profiles in healthy and cancer patients |
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| Relations |
| BioSample |
SAMN03863568 |
| SRA |
SRX1099475 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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