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| Status |
Public on Apr 04, 2016 |
| Title |
PLL-3 miRNA |
| Sample type |
SRA |
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| Source name |
ligament cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Posterior longitudinal ligament
passage: Passage 3
age: 66
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 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.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
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| Description |
small RNA
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| 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
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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 |
SAMN03770044 |
| SRA |
SRX1056663 |
| 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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