|
| Status |
Public on Apr 01, 2022 |
| Title |
MY24_2 |
| Sample type |
SRA |
| |
|
| Source name |
MM1S MM Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MM1S
cell type: multiple myeloma
treatment: YKL-5-124 (98 nM)
treatment time: 24Hr
|
| Treatment protocol |
Treatment with DMSO or YKL for 6 or 24 Hr
|
| Growth protocol |
Cells were grown in 12 well plates in 1 mL of RPMI media with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples (~2.5x10^5 cells) were lysed with trizol and RNA was extracted via the Zymo Directzol RNA extraction kit
RNA-Seq libraries were prepared for sequencing using standard Quantseq 3' library prep protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-Seq for MM1S treated with YKL-5-124 (98 nM) - 24Hr
|
| Data processing |
The RNA-Seq data was first preprocessed with BBDuk for single end samples
All RNA-seq datasets were aligned with HISAT2 and quantified via Cuffquant 2.2 with the hg19 ERCC annotation
Cuffnorm was utilized to normalize data
Top 3 replicates (based on correlation) were used
Inactive genes (no samples with FPKM > 10) were filtered out prior to additional analysis
Genome_build: hg19 ERCC
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 20, 2021 |
| Last update date |
Apr 01, 2022 |
| Contact name |
Charles Yang Lin |
| E-mail(s) |
charles.y.lin@bcm.edu
|
| Phone |
6172764723
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Human Genetics
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE172444 |
CDK7 inhibition interdicts deregulated transcription and cell cycle control in multiple myeloma [Sensitive_MM_Cell_Lines_RNA-seq] |
| GSE172445 |
CDK7 inhibition interdicts deregulated transcription and cell cycle control in multiple myeloma |
|
| Relations |
| BioSample |
SAMN18811501 |
| SRA |
SRX10645562 |
