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Sample GSM5024598 Query DataSets for GSM5024598
Status Public on Mar 22, 2021
Title MM.1S_empty_JQKD82_RNAseq, replicate1
Sample type SRA
 
Source name multiple myeloma cell line
Organism Homo sapiens
Characteristics cell line: MM.1S
tissue: multiple myeloma cell line
transduction: empty vector
Treatment protocol MM.1S cells were treated with 1 µM JQKD82 or DMSO for 48h.
Growth protocol MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description MM1S_MYC_JQKD82_spike_all_fpkm_exprs_norm.txt
Data processing Sequenced reads were aligned to the reference human genome (hg38 or hg19) using RNA-specific STAR aligner.
Reads were further assigned to respective refseq of transcripts using the featureCounts tool or RSEM.
Differential gene expression analysis to compare JQKD82-treated samples with control DMSO-treated samples was performed using DESeq2.
For MYC overexpression experiments, RNA-seq was normalized by a per-cell spike in strategy with ERCC standards.
The data were transformed by Loess normalization with the ERCC transcripts using the R statistical package.
Genome_build: hg38, or hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample
 
Submission date Jan 18, 2021
Last update date Mar 22, 2021
Contact name Hiroto Ohguchi
E-mail(s) ohguchi@kumamoto-u.ac.jp
Phone +81-96-373-6596
Organization name Kumamoto University
Department IRDA
Lab Ohguchi Lab
Street address 2-2-1 Honjo, Chuo-ku
City Kumamoto
State/province Kumamoto
ZIP/Postal code 860-0811
Country Japan
 
Platform ID GPL18573
Series (2)
GSE148047 RNA-seq analysis after JQKD82 treatment in human multiple myeloma cell line MM.1S
GSE148048 ChIP-seq and RNA-seq analyses in human multiple myeloma cell line MM.1S
Relations
BioSample SAMN17373461
SRA SRX9867626

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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