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Sample GSM5360536 Query DataSets for GSM5360536
Status Public on Sep 23, 2021
Title EBNA2 ChIP-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 2
Sample type SRA
 
Source name Ramos B cells
Organism Homo sapiens
Characteristics cell line: Ramos B cells
infection: EBNA+ (B95.8) Epstein-Barr virus (EBV)
chip antibody: EBNA2 (Abcam; ab90543)
Treatment protocol Ramos B cells were infected with EBNA+ (B95.8) Epstein-Barr virus (EBV).
Growth protocol Cells were cultured in 10% FBS supplemented RPMI 1640 medium for 2 weeks.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description ChIP_EBNA2_Ramos_rep2-E02334
Data processing Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19 and hg38) using bowtie2 (version 2.3.4.1) (Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8) (Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS) (Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed using the hg19-blacklist.v2.bed.gz file available at https://github.com/Boyle-Lab/Blacklist/tree/master/lists.
Pooled samples were created by combining the fastq files for replicates 1 and 2.
Genome_build: hg19 (GRCh37)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Peaks called by MACS2 in narrowPeak format.
Supplementary_files_format_and_content: Aligned reads in bigWig format.
 
Submission date Jun 06, 2021
Last update date Oct 23, 2023
Contact name Matthew Weirauch
E-mail(s) Matthew.Weirauch@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Department Center for Autoimmune Genomics and Etiology (CAGE)
Street address 3333 Burnet Avenue
City Cincinnati
State/province Ohio
ZIP/Postal code 45229-3026
Country USA
 
Platform ID GPL24676
Series (2)
GSE148396 Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci
GSE176232 Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [ChIP-seq]
Relations
BioSample SAMN19588399
SRA SRX11078225

Supplementary file Size Download File type/resource
GSM5360536_ChIP_EBNA2_Ramos_rep2.hg19.bw 279.4 Mb (ftp)(http) BW
GSM5360536_ChIP_EBNA2_Ramos_rep2.hg19.narrowPeak.gz 67.0 Kb (ftp)(http) NARROWPEAK
GSM5360536_ChIP_EBNA2_Ramos_rep2.hg38.bw 294.8 Mb (ftp)(http) BW
GSM5360536_ChIP_EBNA2_Ramos_rep2.hg38.narrowPeak.gz 77.6 Kb (ftp)(http) NARROWPEAK
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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