|
| Status |
Public on Dec 11, 2022 |
| Title |
BMS2_D705_S5 |
| Sample type |
SRA |
| |
|
| Source name |
Myeloma Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Myeloma Cell Line
cell subtype: Malignant plasma cell
cell line: MM.1S
|
| Treatment protocol |
MM.1S cells were cultured for 24 hours with 50 μM BMS309403, 50 μM SBFI-26 or the combination in a T25 at a density of 2.5x10^6 cells.
|
| Growth protocol |
MM.1S cells were grown in RPMI-1640 media containing FBS and antibiotic/antimycotic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested in QIAZOL and prepared via Qiagen miRNEASY Kit with DNase On-column digestion (Qiagen; Hildnen, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR 2.6 aligner
Sequenced reads were quantified using an Expectation-Maximization model, and translated to genes
Genes that have fewer than 30 counts were then filtered, and remaining genes median ratio plus 1 normalized, and differential gene expression was evaluated using the algorithm in DESeq2 v3.5 base on median ratio normalization and the negative binomial distribution of gene signal
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample based on the Expectation Maximization algorithm (EM)
|
| |
|
| Submission date |
Dec 11, 2021 |
| Last update date |
Dec 11, 2022 |
| Contact name |
Julie Dragon |
| E-mail(s) |
julie.dragon@uvm.edu
|
| Organization name |
UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
|
| Department |
MMG
|
| Street address |
95 Carrigan Dr
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE190699 |
Fatty acid binding proteins contribute to multiple myeloma cell maintenance through regulation of Myc, the unfolded protein response, and metabolism |
|
| Relations |
| BioSample |
SAMN23898331 |
| SRA |
SRX13384937 |
