|
| Status |
Public on May 15, 2022 |
| Title |
MV4;11_MS40_rep2, RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
MV4;11 cells
|
| Organism |
Homo sapiens |
| Characteristics |
agent: MS40
|
| Treatment protocol |
For compound treatment studies, MV4;11 cells were treated with 0.5 µM of MS40, pomalidomide or MS40N1, relative to DMSO, for 4 days. For the WDR5 knockdown (KD) experiments, MV4;11 cells stably transduced with a doxycycline-inducible WDR5-targeted shRNA (sh#47) or empty vector (shEV) were treated with 0.5 µg/mL of doxycycline (Dox) for four days.
|
| Growth protocol |
MV4;11 cells were grown in RPMI1640 base medium plus 10% FBS and 1% antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using Qiagen RNeasy Mini Kit. Illumina Truseq sample prep kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
All reads were mapped to the human genome (hg19) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept using Samtools. We filtered out reads with a mapping quality score of < 20 for downstream analysis.
Then the quantification was done by salmon (ver 0.14.1). Different expression analysis was done using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates
|
| |
|
| Submission date |
May 25, 2021 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Gang Greg Wang |
| E-mail(s) |
greg_wang@med.unc.edu
|
| Organization name |
University of North Carolina at chapel hill
|
| Department |
UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics
|
| Lab |
gregwang lab
|
| Street address |
405 West Drive
|
| City |
Chapel Hill |
| State/province |
NORTH CAROLINA |
| ZIP/Postal code |
27599-7295 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE175547 |
Discovery of a dual PROTAC for degrading WDR5 and Ikaros oncoproteins as therapeutics [RNA-Seq] |
| GSE175548 |
Discovery of a dual PROTAC for degrading WDR5 and Ikaros oncoproteins as therapeutics |
|
| Relations |
| BioSample |
SAMN19337398 |
| SRA |
SRX10989535 |
