|
| Status |
Public on Sep 01, 2023 |
| Title |
01-day1 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: PBMC
genotype: disease state
treatment: sepsis-ARDS
time point: Blood collected on the 1st day of admission
|
| Extracted molecule |
total RNA |
| Extraction protocol |
flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Single-cell gel bead emulsion generation of blood-derived PBMCs was performed using a chromium controller (10×Genomics), single cell 3' library and gel bead kit V3.1 (10×Genomics).
The resulting GEM libraries were then sequenced on an Illumina Novaseq 6000 using a custom paired-end sequencing mode of 150 bp for the first read and 150 bp for the second read.
The raw data was processed using the Cell Ranger Single-Cell Software Suite (v5.0.0) with default parameters and aligned to the genomic reference.
To maintain data quality, cells were discarded if they had gene counts below 200 or over 5000, or mitochondrial gene expression greater than 15%.
The most variable genes among the single cells were identified, and their log-transformed gene-barcode matrices were subjected to principal component analysis to reduce their dimensionality.
The resulting data was visualized in a t-SNE plot constructed with Seurat (v3.1.1) to differentiate among the PBMC cell types.
Assembly: NOT PROVIDED; REQUESTED
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Sep 01, 2023 |
| Last update date |
Sep 05, 2023 |
| Contact name |
anning chen |
| E-mail(s) |
2021210397@stu.gzhmu.edu.cn
|
| Organization name |
Guangzhou Medical University Cancer Hospital
|
| Street address |
195 West Dongfeng Road
|
| City |
guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE242127 |
A Hub Gene Signature as a Therapeutic Target and Biomarker for Sepsis and Geriatric Sepsis-Induced ARDS Concomitant with COVID-19 Infection |
|
| Relations |
| BioSample |
SAMN37223935 |
| SRA |
SRX21589181 |
