|
| Status |
Public on Mar 13, 2019 |
| Title |
OPM2-Len |
| Sample type |
SRA |
| |
|
| Source name |
Myeloma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OPM2
treatment: 10 uM lenalidomide
|
| Treatment protocol |
Cells as indicated were treated with 10 uM lenalidomide and analyzed on day 3.
|
| Growth protocol |
Cells were cultured at a density of 0.2-1.0 x 106 cells per mL in RPMI 1640 (Corning: 14-030-CV) with 10% FBS, 1% Pen-strep (Corning: 30-002-CI), 1% L-glutamine (Corning: 25005CI), and 1% HEPES (Corning: 25-060-CI). Cell lines were validated using sequencing and phenotypic characterization.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were pelleted at 500g for 10 min and lysed in nuclei lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 ,0.1% IGEPAL)
Nuclei were pelleted at 500g for 30 min and tagmented with 2 mLTn5 (Illumina) for 60 min at 37°C prior to protein digestion with 2 mL 10 mg/mL Proteinase K at 40°C for 60 minutes. Libraries were size selected with SPRI beads (AMPure, Kapa Biosystems) prior to 12 rounds of PCR amplification.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
tagmentation accessible DNA
|
| Data processing |
ATAC-seq FASTQ files were aligned to the human genome (GRCh37) using bowtie2 (v2.2.6).
Mapped SAM files were converted to BAM files and putative PCR duplicates were marked using SAMtools (v1.7)
Regions with accessible chromatin were determined with MACS2 (v2.1.0.20151222) with the following parameters "-g hs -q 0.01".
The union of all regions with chromatin accessibility were determined in R/Bioconductor (v3.4.4) using the GenomicRanges package (v1.30.3).
Data were normalized for reads per peak per million (RPPM) = reads x 106 / (total # of autosomal reads x fraction of reads in peaks)
Genome_build: GRCh37
|
| |
|
| Submission date |
Oct 29, 2018 |
| Last update date |
Mar 14, 2019 |
| Contact name |
Benjamin G Barwick |
| E-mail(s) |
benjamin.barwick@emory.edu
|
| Phone |
(404) 285-2964
|
| Organization name |
Emory University
|
| Department |
Hematology and Medical Oncology
|
| Lab |
Barwick Lab
|
| Street address |
1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE121912 |
Multiple myeloma immunoglobulin lambda translocations portend poor prognosis |
|
| Relations |
| BioSample |
SAMN10341376 |
| SRA |
SRX4949876 |
