|
| Status |
Public on Jul 22, 2020 |
| Title |
Pom_72h-3 |
| Sample type |
SRA |
| |
|
| Source name |
MM.1S, human cell line, peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
disease: multiple myeloma
genotype/variation: Wild type
treatment: 1 uM pomalidomide for 72 hours
|
| Treatment protocol |
MM.1S cells were treated with 1 µM pomalidomide for 24, 48, or 72 hours. Alternatively, MM.1S cells were transduced with recombinant lentivirus expressing shRNA against ARID2 or Aiolos for 72 hours.
|
| Growth protocol |
MM.1S cells were maintained in ATCC-formulated RPMI 1640 with 10% FBS and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Sepasol-RNA I Super G (Nacalai Tesque) and then cleaned up using RNeasy mini kit (Qiagen).
The libraries were prepared using by TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The resulting reads were adapter-trimmed and mapped on hg38 using CLC Genomics Workbench version 11.0 (Qiagen). TPM was also calculated using CLC Genomics Workbench.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values of coding genes that expressed (TPM >0) in one or more samples.
|
| |
|
| Submission date |
Feb 12, 2019 |
| Last update date |
Jul 22, 2020 |
| Contact name |
Yuki Yamaguchi |
| E-mail(s) |
yyamaguc@bio.titech.ac.jp
|
| Organization name |
Tokyo Institute of Technology
|
| Department |
School of Life Science and Technology
|
| Street address |
Nagatsutacho 4259
|
| City |
Yokohama |
| ZIP/Postal code |
226-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE126463 |
mRNA-sequencing for MM.1S cells that were treated with pomalidomide or were expressing shRNA against ARID2 or Aiolos. |
|
| Relations |
| BioSample |
SAMN10921787 |
| SRA |
SRX5369649 |
