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Sample GSM5322194 Query DataSets for GSM5322194
Status Public on May 19, 2021
Title A549 S2 rep1 [C1]
Sample type SRA
 
Source name A549 S2
Organism Homo sapiens
Characteristics cell line: A549
treatment: after incubation with EVs isolated from hyperinflammatory (S2)
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) [email protected]
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 SAMN19250187
SRA SRX10931874

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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