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Sample GSM5729318 Query DataSets for GSM5729318
Status Public on Dec 11, 2022
Title SBF2_D708_S8
Sample type SRA
 
Source name Myeloma Cell Line
Organism Homo sapiens
Characteristics cell type: Myeloma Cell Line
cell subtype: Malignant plasma cell
cell line: MM.1S
Treatment protocol MM.1S cells were cultured for 24 hours with 50 μM BMS309403, 50 μM SBFI-26 or the combination in a T25 at a density of 2.5x10^6 cells.
Growth protocol MM.1S cells were grown in RPMI-1640 media containing FBS and antibiotic/antimycotic
Extracted molecule total RNA
Extraction protocol Total RNA was harvested in QIAZOL and prepared via Qiagen miRNEASY Kit with DNase On-column digestion (Qiagen; Hildnen, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR 2.6 aligner
Sequenced reads were quantified using an Expectation-Maximization model, and translated to genes
Genes that have fewer than 30 counts were then filtered, and remaining genes median ratio plus 1 normalized, and differential gene expression was evaluated using the algorithm in DESeq2 v3.5 base on median ratio normalization and the negative binomial distribution of gene signal
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample based on the Expectation Maximization algorithm (EM)
 
Submission date Dec 11, 2021
Last update date Dec 11, 2022
Contact name Julie Dragon
E-mail(s) julie.dragon@uvm.edu
Organization name UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
Department MMG
Street address 95 Carrigan Dr
City Burlington
State/province VT
ZIP/Postal code 05405
Country USA
 
Platform ID GPL18460
Series (1)
GSE190699 Fatty acid binding proteins contribute to multiple myeloma cell maintenance through regulation of Myc, the unfolded protein response, and metabolism
Relations
BioSample SAMN23898328
SRA SRX13384940

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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