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Sample GSM3449816 Query DataSets for GSM3449816
Status Public on Mar 13, 2019
Title Karpas620-Ctrl
Sample type SRA
 
Source name Myeloma cell line
Organism Homo sapiens
Characteristics cell line: Karpas620
treatment: none
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 SAMN10341396
SRA SRX4949856

Supplementary file Size Download File type/resource
GSM3449816_Karpas620-Ctrl.union.0.01.rppm.bw 157.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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