|
| Status |
Public on Jul 30, 2021 |
| Title |
2-RNAseq-568 |
| Sample type |
SRA |
| |
|
| Source name |
THP1
|
| Organism |
Homo sapiens |
| Characteristics |
condition: SN_IMR902
|
| Treatment protocol |
Cells were infected with virus or cultivated in conditioned medium for 5 days (THP-1: 3 days) and cell pellets were collected for RNA extraction. THP1 VIS samples were split into CD86+ and CD86- fractions using surface labelung with a CD86-biotin antibody and anti-biotin Microbeads from Miltenyi, following the manufacturer´s instructions.
|
| Growth protocol |
A549 and Wi38 cells were cultivated in DMEM supplemented with 10% FBS and Pen-Strep antibiotics; THP-1 cells were cultivated in RPMI-1640 supplemented with 10% FBS and Pen-Strep antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit
Libraries were prepared by BGI or DKFZ sequencing core facility according to Illumina's TruSeq RNA kit (RS-122-2001) instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
supernatant/conditioned medium of proliferating IMR90 fibroblasts
SN_IMR902
THP1_norm_counts
|
| Data processing |
Transcript quantification using salmon (Patro et al.)
Transcript import using tximeta (Love et al.) or tximport packages (Soneson et al.).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized transcript counts for every gene and every sample
|
| |
|
| Submission date |
Jan 26, 2021 |
| Last update date |
Jul 30, 2021 |
| Contact name |
Clemens Schmitt |
| E-mail(s) |
clemens.schmitt@charite.de
|
| Organization name |
Charite
|
| Department |
Hematology, Oncology, Tumorimmunology
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE165532 |
Virus-induced senescence is a central pathogenic principle and therapeutic target in COVID-19 disease |
|
| Relations |
| BioSample |
SAMN17576135 |
| SRA |
SRX9939148 |
