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Sample GSM1708782 Query DataSets for GSM1708782
Status Public on Apr 04, 2016
Title PLL-3 miRNA
Sample type SRA
Source name ligament cells
Organism Homo sapiens
Characteristics tissue: Posterior longitudinal ligament
passage: Passage 3
age: 66
gender: male
Growth protocol Normal posterior longitudinal ligament were dissected during the surgery, all tissues were obtained with written informed consent signed by the donors voluntarily for research. Ligaments were further cut into pieces and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 3 were used for the experiments.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA library had been size selected by PAGE Gel electrophoresis for miRNA sequencing. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Ion Torrent Proton
Description small RNA
Data processing [miRNA] We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
[miRNA] Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo Sapiens miRNA database and GRCH37.p13 genome.
[miRNA] count counting
Genome_build: miRBase 21.0
Supplementary_files_format_and_content: TXT file contain counts for each sample
Submission date Jun 11, 2015
Last update date May 15, 2019
Contact name Chen Xu
Phone +86-13774294166
Organization name The Second Military Medical University
Street address No, 800, Rd. Xiangyin
City Shanghai
ZIP/Postal code 200433
Country China
Platform ID GPL17303
Series (1)
GSE69787 Transcriptome and Micronome analysis of OPLL
BioSample SAMN03770044
SRA SRX1056663

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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