|
| Status |
Public on Sep 13, 2024 |
| Title |
biol rep 1, Donor 1, PBMCs, Spike protein |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell line: peripheral blood mononuclear cells
genotype: treated with Spike protein
treatment: total RNA
|
| Treatment protocol |
Then PBS, spike protein, IL-2 (100 IU/mL), and IL-2 (100 IU/mL) combined with spike protein (10 μM) were added to PBMCs. After 16 hrs of incubation, the supernatant was collected for cytokine detection.
|
| Growth protocol |
Human peripheral blood mononuclear cells (PBMCs) were adjusted to 1×10E6 cells/mL RPMI-1640 medium, and the PBMCs were inoculated into 24-well plates at 400 μL per well.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol. To ensure the quality of the library, the effective concentration of the library is higher than 2nM.
RNA libraries for RNA-seq were prepared using NEB method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
biol rep 1
Spike protein
Sample 2
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the hg38.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 29, 2023 |
| Last update date |
Sep 13, 2024 |
| Contact name |
Chao Niu |
| E-mail(s) |
chaoniu@jlu.edu.cn
|
| Phone |
+8643188782046
|
| Organization name |
The First Hospital of Jilin University
|
| Department |
Cancer Center
|
| Street address |
Xinmin Street #1
|
| City |
Changchun |
| State/province |
Jilin |
| ZIP/Postal code |
130021 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE241843 |
SARS-CoV-2 spike protein induces the cytokine release syndrome by stimulating T cells to produce more IL-2 |
|
| Relations |
| BioSample |
SAMN37186724 |
| SRA |
SRX21503943 |
