|
| Status |
Public on Oct 31, 2016 |
| Title |
BM clone_2 |
| 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 |
SAMN03603430 |
| SRA |
SRX1017368 |
