|
| Status |
Public on Jun 09, 2022 |
| Title |
COVID-19 patient_2 |
| Sample type |
SRA |
| |
|
| Source name |
COVID-19 patient_2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells
diagnosis: COVID-19
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation of leukocytes from ten COVID-19 patients on day1 and five healthy controls in the Osaka Covid-19 Cohort was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PBMCs derived from COVID-19 patient_2
|
| Data processing |
Sequencing was performed on an Illumina NovaSeq 6000 platform in 101- base paired-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.0.13, in combination with Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM processed value in csv file
|
| |
|
| Submission date |
Jul 10, 2021 |
| Last update date |
Jun 09, 2022 |
| Contact name |
Daisuke Okuzaki |
| E-mail(s) |
dokuzaki@biken.osaka-u.ac.jp
|
| Phone |
+81-6-6879-4935
|
| Organization name |
Osaka univ.
|
| Department |
Immunology Frontier Research Center
|
| Lab |
Human Immunology （Single Cell Genomics)
|
| Street address |
Yamadaoka 3-1
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE192707 |
Resistin Forms a Network with Cytokines Associated with Endothelial Damage and Worse Outcome in COVID-19 |
|
| Relations |
| BioSample |
SAMN20163928 |
| SRA |
SRX13572880 |
