|
| Status |
Public on Sep 23, 2021 |
| Title |
EBNA2 ChIP-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 1 |
| 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_rep1-E02333
|
| 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 |
SAMN19588400 |
| SRA |
SRX11078224 |
