|
| Status |
Public on Mar 31, 2022 |
| Title |
Combination4 |
| Sample type |
SRA |
| |
|
| Source name |
U87ΔEGFR and Raw264.7
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: human glioblastoma cell and murine macrophage cell
treatment: GSI and oHSV (DAPT 25uM and 0.5MOI of rHSVQ)
|
| Treatment protocol |
U87ΔEGFR cells were infected with 0.5 MOI of rHSVQ in the presence of DMSO or DAPT (25µM) for 1 hour. Media was changed into new media containing DMSO or DAPT and overlaid with Raw264.7 cells at a 1:2 ratio for 12 hours.
|
| Growth protocol |
Cells were cultured in DMEM/RPMI containing 2% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We isolated total RNA using the RNeasy kit (Qiagen, Germantown, MD) and RNase-free DNase set (Qiagen)
Illumina sequencing and library prep was carried out at Novogene Bioinformatics Technology Co., Ltd., in Beijing, China.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Combination4
|
| Data processing |
To analyze the RNAseq of co-culture samples, we mapped the sequencing reads to Human and Mouse genome references using STAR mapper (version 2.5.3a) to generate bam files.
XenofilteR (version 1.6) was further used for computational deconvolution of the mouse and human reads.
The raw count of reads for the genomic features was evaluated by htseq-count (version 0.9.1).
Genome_build: Human: Grch38; Mouse: Grch38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample
|
| |
|
| Submission date |
Sep 01, 2021 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Yoshihiro Otani |
| Organization name |
Okayama University Hospital
|
| Department |
Neurological Surgery
|
| Street address |
2-5-1, Shikata, Kita-ku
|
| City |
Okayama |
| ZIP/Postal code |
7008558 |
| Country |
Japan |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE183221 |
Identification of gene expression alteration in macrophage cells with oncolytic HSV |
|
| Relations |
| BioSample |
SAMN21173714 |
| SRA |
SRX11987936 |
