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Sample GSM4979742 Query DataSets for GSM4979742
Status Public on Feb 24, 2021
Title ST_Kasumi1_CRYBMIM-1
Sample type SRA
 
Source name Kasumi1 cell line
Organism Homo sapiens
Characteristics cell type: leukemia cell
cell line: Kasumi1
treatment: CRYBMIM peptide
time point: 1hr
Treatment protocol The indicated 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 The indicated 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 To generate a genome annotation, we combined the UCSC knownGen, Ensembl 71, and MISO v.2.0 annotations.
We mapped all reads to the merged genome annotation and obtained gene expression estimates using RSEM v.1.2.4 modified to invoke Bowtie v.1.0.0 through the ‘-v 2’ option.
We normalized all expression estimates via the trimmed mean of M values (TMM) method.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with 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)
GSE163469 Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia [RNAseq_4cellLines]
GSE163470 Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia
Relations
BioSample SAMN17112371
SRA SRX9702088

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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