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Sample GSM2256387 Query DataSets for GSM2256387
Status Public on Jul 31, 2017
Title JJN3 overexpressing RASSF4
Sample type SRA
 
Source name Human Multiple Myeloma Cell Lines
Organism Homo sapiens
Characteristics cell type: Multiple Myeloma
cell line: JJN3
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany) according to manufactures’ instructions.
The RNA sequencing library preparation was done with 150ng of input RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit. Paired-end RNA-seq were performed with illumina NextSeq sequencing instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description JJN3RF4Dox
Data processing RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner. All statistical analyses were performed with the statistics software R and R packages developed by BioConductor project. The expression level of each gene was summarized and normalized using DESeq2 R/Bioconductor package. Differential expression analysis were performed using DESeq2 pipeline. P values were adjusted to control the global FDR across all comparisons with the default option of the DESeq2 package. Genes were considered differentially expressed if they had an adjusted p-value of 0.05 and a fold change of 1.5.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts as provided by DESeq2.
 
Submission date Aug 01, 2016
Last update date May 15, 2019
Contact name Jerome Moreaux
E-mail(s) jerome.moreaux@igh.cnrs.fr
Organization name CHRU Montpellier
Department Biological Hematology
Lab Laboratory for Monitoring Innovative Therapies
Street address 80 Av. Augustin Fliche
City Montpellier
ZIP/Postal code 34295
Country France
 
Platform ID GPL18573
Series (1)
GSE85020 Epigenetic silencing of the tumor suppressor RASSF4 favors multiple myeloma progression
Relations
BioSample SAMN05467346
SRA SRX1992413

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

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