|
| Status |
Public on May 19, 2021 |
| Title |
A549 S1 rep1 [B1] |
| Sample type |
SRA |
| |
|
| Source name |
A549 S1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
treatment: after incubation with EVs isolated from presymptomatic (S1)
genotype/variation: wild type
|
| Treatment protocol |
EVs were isolated from 1 ml of pooled plasma from each of the clinical stages, which included healthy controls (HC), as well as S1, S2, S3 and S4 phases of COVID-19. Cells were incubated with culture medium containing the appropriate concentrations of EVs in 12-well plates for 12 h at 37 oC. At the end of the incubation, cell culture medium was aspirated. The cells were washed three times with ice-cold 1XPBS.
|
| Growth protocol |
HepG2 and A549 cells were obtained from the American Type Culture Collection. HepG2 cells were maintained in DMEM (high glucose) medium (Gibco) supplemented with 10% FBS, and A549 were maintained in RPMI 1640 medium (Gibco) supplemented with 10% FBS. Cells were cultured at 37 oC in an atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from cells inactivated with 1 ml of TRIzol reagent. For each phase separation, 0.2 ml of chloroform was added and the aqueous phase was collected in fresh tubes and mixed with 0.5 ml of isopropyl alcohol for pelleting RNA. RNA pellets were washed with 75% ethanol and digested with DNase for 30 min to remove DNA contamination, then pelleted via addition of NaOAC and LiCl. RNA pellets were then washed with 75% ethanol and reconstituted in nuclease-free water.
RNAs were reverse transcribed into cDNAs and PromethION library preparation was performed based on the manufacturer's instructions for the barcoding cNDA (SQK-LSK109, EXP-NBD104 and EXP-NBD114).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Guppy (v3.2.4) was used for real-time base-calling
Adaptor sequence and barcode sequence were trimmed using Qcat for clean data, then aligned to human whole genome using minimap2 with default parameters.
The number of reads aligned to human genes was calculated using BEDtools multicov with human gene annotation file GFF (GENCODE v37)
Genome_build: GRCH38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 19, 2021 |
| Last update date |
May 20, 2021 |
| Contact name |
Guanghou Shui |
| E-mail(s) |
ghshui@genetics.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
|
| Street address |
Bei Chen Road(west)
|
| City |
BEIJING |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE174668 |
A multi-omics investigation on the composition and physiological function of extracellular vesicles along the temporal trajectory of COVID-19 |
|
| Relations |
| BioSample |
SAMN19250190 |
| SRA |
SRX10931871 |
