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Sample GSM1674772 Query DataSets for GSM1674772
Status Public on Oct 31, 2016
Title BM clone_3
Sample type SRA
 
Source name Bone marrow prone clone
Organism Homo sapiens
Characteristics cell type: multiple myeloma bone marrow prone clone
Treatment protocol None
Growth protocol BM-prone and EMD-prone MM cell lines were developed by serial in vivo selection.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from EMD-prone and BM-prone cell lines using RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols
poly-A selection and cDNA synthesis were performed, followed by library preparation using Illumina TruSeq RNA Sample Prep Kit, sequencing (75bp paired reads), and sample identification for quality control.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description bone marrow clone obtained after in vivo selection
Data processing We used Bcbio_nextgen (https://github.com/chapmanb/bcbio-nextgen/) to process the RNA-seq data. Briefly, cutadapt (https://github.com/marcelm/cutadapt/) was used to trim adapters; trimmed reads were aligned to Human reference genome (GRCh37) with tophat2; read count for each gene was calculated by HT-seq. Genes with low expression (FPKM < 1 across all samples) were filtered out. GSEA was used to identify differentially expressed mRNA signatures, with false discovery rate (FDR) <0.25 and P value <0.05.
Genome_build: GRCh37
Supplementary_files_format_and_content: RPKM files
 
Submission date May 05, 2015
Last update date May 15, 2019
Contact name Aldo Roccaro
E-mail(s) roccaroaldo@gmail.com
Phone 6176326733
Organization name Dana-Farber Cancer Institute
Street address 450 Brookline Av
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL11154
Series (1)
GSE68538 CXCR4 regulates extra-medullary myeloma through epithelial-mesenchymal transition-like transcriptional activation
Relations
BioSample SAMN03603431
SRA SRX1017369

Supplementary file Size Download File type/resource
GSM1674772_BM_clone_3.rpkm.gz 1.6 Mb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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