|
| Status |
Public on Mar 12, 2023 |
| Title |
PBMC |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: COVID-19 patient
cell type: peripheral blood mononuclear cell (PBMC)
|
| Growth protocol |
Cells get from COVID-19 patient
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were collected ad resuspended in DPBS with 0.04% BSA. Then, cells suspensions (500-1000 cells per microliter) were loaded on a Chromium Single Cell Controller (10x Genomics) to obtain single-cell gel beads in emulsion (GEMs) by using Single Cell 3’ Library and Gel Bead Kit V2 (10x genomics, 120237). Captured cDNAs were lysed and the released RNA were barcoded through reverse transcription in singular GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleaned by DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared by Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics, 120237) following the manufacturer’s instruction. Sequencing was operated on an Illumina HiSeq X Ten
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using STAR
Fastq reads were aligned to the genome using STARsolo with the setting ‘--outSAMattributes NH HI AS nM CR CY UR UY --readFilesCommand zcat --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1’.
Genome_build: hg38
|
| |
|
| Submission date |
Mar 17, 2020 |
| Last update date |
Mar 12, 2023 |
| Contact name |
Jiangping He |
| E-mail(s) |
he_jiangping@grmh-gdl.cn
|
| Organization name |
Guangzhou Institutes of Biomedicine and Health (GIBH), CAS
|
| Street address |
Kai yuan avenue 190
|
| City |
GuangZhou |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE146943 |
Single-cell sequencing of pleural effusion reveals immune response of COV2019 infection |
|
| Relations |
| BioSample |
SAMN14394637 |
