|
| Status |
Public on May 16, 2024 |
| Title |
Calu3 cells - Sin Nombre virus - 48hrs - rep 1 [Sample 3_CA13] |
| Sample type |
SRA |
| |
|
| Source name |
Calu3 cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Infected
cell type: Calu3
|
| Treatment protocol |
Three types of cells described above were either uninfected or infected with ANDV, SNV and HTNV and treated or un-treated with drugs at 48 hrs
|
| Growth protocol |
Cells were cultured in EMEM+15% FBS+1% Pen-Strep+1% MEM NEAA+1% L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were harvested in TriZol and RNA was extracted using the BioRad RNA Mini kit
Libraries were prepared with KAPA Stranded mRNA-Seq Kit followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina reads from all the samples were mapped to human reference genome by STAR v2.7.9a and read counts per gene were quantified using human genome GRCh38.107 GTF file to generate raw reads counts. Differential expression analysis was performed using DESeq2 v1.34.0 in R v4.1.2
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 16, 2023 |
| Last update date |
May 16, 2024 |
| Contact name |
ARJIT VIJEY JEYACHANDRAN |
| E-mail(s) |
ajeyachandran99@g.ucla.edu
|
| Phone |
3108252020
|
| Organization name |
UCLA
|
| Street address |
Tiverton Ave
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE232641 |
Evaluating Differential Tropism, Pathogenesis, and Antiviral Agents of Hemorrhagic Fever Renal Syndrome and Cardiopulmonary Syndrome Causative Hantaviruses: Andes virus (ANDV), Sin Nombre virus (SNV), and Hantaan virus (HTNV) |
|
| Relations |
| BioSample |
SAMN35115863 |
| SRA |
SRX20377890 |
