|
| Status |
Public on Aug 06, 2019 |
| Title |
F3_A_1 |
| Sample type |
SRA |
| |
|
| Source name |
Cerebrospinal fluid (CSF)
|
| Organism |
Homo sapiens |
| Characteristics |
evs enrichment method: Size exclusion chromatography (SEC)
total rna extraction method: mirVana PARIS kit (Ambion)
tissue: Cerebrospinal fluid (CSF)
|
| Treatment protocol |
CSF samples were obtained via lumbar puncture, centrifuged to remove contaminant cells (500 xg for 10 min), aliquoted, and immediately stored at -80°C until their processing. Then, samples were thawed together at 4°C, mixed to generate a pool of samples, centrifuged to remove cell debris (3,000 xg for 15 min at 4°C), and aliquoted in a 200 µl format (cleared CSF). Before total RNA extraction some of them incorporated a EVs enrichment step, as detailed in SAMPLES section.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVana PARIS kit (Ambion) and the Plasma/Serum RNA Purification kit (Norgen), as detailed in the SAMPLES section
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
smallRNA
ProcessedData_Quatified-Counts_JF14.xls
|
| Data processing |
FASTQs were trimmed for adapters and quality score.
We used bowtie 1.01 to align reads against the human genome with the corresponding annotations (GRCh38/GENCODE-v26).
Mapped reads were quantified to GENCODE-v26 using Partek E/M method, so the processed data file contains counts values normalized by Partek E/M method
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table in Excel, Quantified read counts
|
| |
|
| Submission date |
Nov 01, 2018 |
| Last update date |
Aug 06, 2019 |
| Contact name |
Ana Maria Aransay |
| E-mail(s) |
amaransay@cicbiogune.es
|
| Phone |
0034944061325
|
| Organization name |
CIC bioGUNE
|
| Department |
Genome Analysis Platform
|
| Street address |
Parque tecnologico de Bizkaia, Building 801-A
|
| City |
Derio |
| State/province |
BIZKAIA |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE122068 |
Comparison of methods for the characterization of miRNAs from 200 µl of cerebrospinal fluid |
|
| Relations |
| BioSample |
SAMN10359211 |
| SRA |
SRX4965575 |
