|
| Status |
Public on Mar 22, 2021 |
| Title |
MM.1S_DMSO_RNAseq, replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
multiple myeloma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MM.1S
tissue: multiple myeloma cell line
|
| Treatment protocol |
MM.1S cells were treated with 1 µM JQKD82 or DMSO for 48h.
|
| Growth protocol |
MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were aligned to the reference human genome (hg38) using RNA-specific STAR aligner.
Reads were further assigned to respective hg38 refseq of transcripts using the featureCounts tool.
Differential gene expression analysis to compare JQKD82-treated samples with control DMSO-treated samples was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and normalized counts for each sample
|
| |
|
| Submission date |
Apr 03, 2020 |
| Last update date |
Mar 22, 2021 |
| Contact name |
Hiroto Ohguchi |
| E-mail(s) |
ohguchi@kumamoto-u.ac.jp
|
| Phone |
+81-96-373-6596
|
| Organization name |
Kumamoto University
|
| Department |
IRDA
|
| Lab |
Ohguchi Lab
|
| Street address |
2-2-1 Honjo, Chuo-ku
|
| City |
Kumamoto |
| State/province |
Kumamoto |
| ZIP/Postal code |
860-0811 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE148047 |
RNA-seq analysis after JQKD82 treatment in human multiple myeloma cell line MM.1S |
| GSE148048 |
ChIP-seq and RNA-seq analyses in human multiple myeloma cell line MM.1S |
|
| Relations |
| BioSample |
SAMN14533619 |
| SRA |
SRX8053115 |
