|
| Status |
Public on Feb 24, 2021 |
| Title |
RNA_MV411_CREBMIM_4C |
| Sample type |
SRA |
| |
|
| Source name |
MV411 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: leukemia cell
cell line: MV411
treatment: CREBMIM peptide
time point: 4hr
|
| Treatment protocol |
MV411 cells were resuspended to a concentration of 15 million cells/5 mL of working media. Peptide suspensions were made in PBS of CREBMIM and CRYBMIM peptides from lyophilized product. Peptide suspensions or PBS control were added directly to working media to a final concentration of 20 mM. Cells were incubated with peptide or control for 1h or 4h at 37°C and then resuspended in PBS.
|
| Growth protocol |
MV411 cells were cultured at 37°C in 5% CO2 humidified atmosphere in RPMI medium supplemented with 10% fetal bovine serum (FBS), antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin), and L-glutamine (1%).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by TRIzol extraction
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.
|
| |
|
| Submission date |
Dec 18, 2020 |
| Last update date |
Feb 24, 2021 |
| Contact name |
Richard Koche |
| E-mail(s) |
kocher@mskcc.org
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Street address |
417 E. 68th St.
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE163466 |
Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia [RNAseq_MV411] |
| GSE163470 |
Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN17112340 |
| SRA |
SRX9702061 |
