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| Status |
Public on Apr 04, 2016 |
| Title |
OPLL-3 mRNA |
| Sample type |
SRA |
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| Source name |
ligament cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Ossified Posterior longitudinal ligament
passage: Passage 3
age: 63
gender: male
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
Total RNA
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| 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
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| Submission date |
Jun 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chen Xu |
| E-mail(s) |
chenxu8836@hotmail.com
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| Phone |
+86-13774294166
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| Organization name |
The Second Military Medical University
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| Street address |
No, 800, Rd. Xiangyin
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| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE69787 |
Transcriptome and Micronome analysis of OPLL |
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| Relations |
| BioSample |
SAMN03770041 |
| SRA |
SRX1056660 |
| 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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