|
Status |
Public on Oct 31, 2016 |
Title |
EMD clone_2 |
Sample type |
SRA |
|
|
Source name |
Extra medullary prone clone
|
Organism |
Homo sapiens |
Characteristics |
cell type: multiple myeloma extra medullary 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 |
extra medullary 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 |
SAMN03603433 |
SRA |
SRX1017371 |