|
| Status |
Public on Nov 11, 2021 |
| Title |
PLL_miRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Exosomes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal posterior longitudinal ligament (PLL)tissue
molecule subtype: Exosomes
|
| Treatment protocol |
no treatment
|
| Growth protocol |
10%FBS high-glucose DMEM were used as culture medium for primary ligament cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage. After 2 passages, the primary cells were ready to perform exosome collection. For exosome collection, we use 1% exosome free FBS/DMEM for culture, the medium were collected at a 3-days interval for exosome collection.
|
| 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.
Proton Sequencing Protocol
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
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.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and GRCh38. genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Nov 11, 2021 |
| Contact name |
Chen Xu |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE113632 |
MicroRNA profiling and analysis of primary OPLL cell derived exosomes |
|
| Relations |
| BioSample |
SAMN08979294 |
| SRA |
SRX3993634 |
