|
| Status |
Public on Mar 22, 2021 |
| Title |
MM.1S_empty_DMSO_RNAseq, replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
multiple myeloma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MM.1S
tissue: multiple myeloma cell line
transduction: empty vector
|
| 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) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MM1S_MYC_JQKD82_spike_all_fpkm_exprs_norm.txt
|
| Data processing |
Sequenced reads were aligned to the reference human genome (hg38 or hg19) using RNA-specific STAR aligner.
Reads were further assigned to respective refseq of transcripts using the featureCounts tool or RSEM.
Differential gene expression analysis to compare JQKD82-treated samples with control DMSO-treated samples was performed using DESeq2.
For MYC overexpression experiments, RNA-seq was normalized by a per-cell spike in strategy with ERCC standards.
The data were transformed by Loess normalization with the ERCC transcripts using the R statistical package.
Genome_build: hg38, or hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample
|
| |
|
| Submission date |
Jan 18, 2021 |
| 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 |
GPL18573 |
| 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 |
SAMN17373462 |
| SRA |
SRX9867625 |
