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Sample GSM1708779 Query DataSets for GSM1708779
Status Public on Apr 04, 2016
Title OPLL-3 mRNA
Sample type SRA
Source name ligament cells
Organism Homo sapiens
Characteristics tissue: Ossified Posterior longitudinal ligament
passage: Passage 3
age: 63
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 cDNA library construction.
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 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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description Total RNA
Data processing [mRNA] Reads filtering under criteria removing reads with 20% of the base quality lower than 13
[mRNA] Mapsplice v2.1.8 mapping to reference genome
[mRNA] count counting
Genome_build: hg19_GRCh37
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 SAMN03770041
SRA SRX1056660

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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