|
| Status |
Public on Feb 21, 2022 |
| Title |
LPS-RA FLSs EVs 2 |
| Sample type |
SRA |
| |
|
| Source name |
LPS-RA FLSs EVs
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Fibroblast-like synoviocytes derived extracellular vesicles
treatment: LPS-RA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from extracellular vesicles pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer(NanoDrop Technologies, Wilmington, DE). Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135 155 bp PCR amplified fragments (corresponding to 15 35 nt small RNAs).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with bowtie software.
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ).
Raw reads were normalized by calculated CPM value
Genome_build: miRBase Release 22
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample.
|
| |
|
| Submission date |
Oct 11, 2021 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Yixiong Chen |
| E-mail(s) |
chenyx376@mail2.sysu.edu.cn
|
| Organization name |
The Third Affiliated Hospital of Sun Yat-sen University
|
| Street address |
No. 600 Tianhe Road, Tianhe District
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE185672 |
Human Fibroblast-Like Synoviocytes Derived Extracellular Vesicles miRNA sequencing |
|
| Relations |
| BioSample |
SAMN22215951 |
| SRA |
SRX12571563 |
