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Sample GSM2702714 Query DataSets for GSM2702714
Status Public on Sep 01, 2017
Title 26-RBL-Donor-1-P3-D2
Sample type SRA
 
Source name Primary B cells infected with EBV
Organism Homo sapiens
Characteristics cell type: Primary B cells
ebv strain: P3HR1
Treatment protocol Primary B cells were purified from human blood collars using RosetteSep and EasySep B cell kits (StemCell). B cells are infected with EBV virus, titered to ensure >90% of B cells are infected.
Growth protocol Cells were grown in RPMI media supplemented witth 10% Fetal Bovine Serum, 2 mM glutamine, 1X penicillin and streptomycin.
Extracted molecule genomic DNA
Extraction protocol ATAC-seq was performed on samples as per described in Buenrostro et al, Nature Methods 2013.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description ATAC-seq
Data processing Sequencing adapters were trimmed using Trim Galore at default parameters
Paired-end reads were mapped to hg19 using bowtie, with parameters "--chunkmbs 2000 -X 2000", and reads mapping to chrM were removed
Ataqc was used to perform quality control of samples, using default parameters
All reads were subsampled to the lowest sample (13.8 million reads), for sample uniformity
For visualization of the bam files on IGV, igvtools count was used to generate IGV specific TDF visualization files
ngs.plot was used to plot the ATAC reads around EBV Super Enhancers (from Zhou et al 2015) using the following parameters "-N 20 -FL 183 -RB 0.05 -MW 5 -IN 1"
Genome_build: hg19
Supplementary_files_format_and_content: Uniformly sub-sampled bam files, mapped to hg19, for EBV transformed human primary B cells from 1 donor; TDF file
 
Submission date Jul 13, 2017
Last update date May 15, 2019
Contact name Sizun Jiang
Organization name BIDMC/Harvard
Street address 3 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL18573
Series (1)
GSE101426 3D genome landscape of Epstein-Barr Virus oncoproteins and virus activated NF-kB in lymphoblastoid cells
Relations
BioSample SAMN07350559
SRA SRX3003805

Supplementary file Size Download File type/resource
GSM2702714_sampled-26-RBL-Donor-1-P3-D2.hqaa.bam 614.2 Mb (ftp)(http) BAM
GSM2702714_sampled-26-RBL-Donor-1-P3-D2.hqaa_sorted.bam.count.tdf.gz 100.8 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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