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Status |
Public on Sep 01, 2017 |
Title |
27-RBL-Donor-1-P3-D5 |
Sample type |
SRA |
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Source name |
Primary B cells infected with EBV
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Organism |
Homo sapiens |
Characteristics |
cell type: Primary B cells ebv strain: P3HR1
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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.
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Growth protocol |
Cells were grown in RPMI media supplemented witth 10% Fetal Bovine Serum, 2 mM glutamine, 1X penicillin and streptomycin.
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Extracted molecule |
genomic DNA |
Extraction protocol |
ATAC-seq was performed on samples as per described in Buenrostro et al, Nature Methods 2013.
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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Description |
ATAC-seq
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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
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Submission date |
Jul 13, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Sizun Jiang |
Organization name |
BIDMC/Harvard
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Street address |
3 Blackfan Circle
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
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Platform ID |
GPL18573 |
Series (1) |
GSE101426 |
3D genome landscape of Epstein-Barr Virus oncoproteins and virus activated NF-kB in lymphoblastoid cells |
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Relations |
BioSample |
SAMN07350558 |
SRA |
SRX3003806 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2702715_sampled-27-RBL-Donor-1-P3-D5.hqaa.bam |
619.3 Mb |
(ftp)(http) |
BAM |
GSM2702715_sampled-27-RBL-Donor-1-P3-D5.hqaa_sorted.bam.count.tdf.gz |
104.7 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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