|
| Status |
Public on Mar 12, 2024 |
| Title |
SPI1 ChIP-seq: AG876 Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
AG876
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AG876
virus type: EBV2
virus strain: AG876
chip antibody: CST 2266
|
| Growth protocol |
The AG876, Jiyoye, and GM12878 cell lines were grown in RPMI medium supplemented with 2 mM L-glutamine, 10% FBS, 1X antibiotic-antimycotic , and 0.2% Normocin at 200,000 – 500,000 viable cells/mL. Cells were incubated in flasks at 37C with 5% carbon dioxide in an upright position with vented.
|
| 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 |
| |
|
| Data processing |
We performed quality control of raw sequencing reads using the ChIP-seq transcription factor Pipeline v2.2.0 from the ENCODE Project (https://www.encodeproject.org/pipelines/).
ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2. Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using the default parameters of MACS2 (p < 0.01).
The ENCODE blacklist region was removed upon establishing the final peak set.
Irreproducibility Discovery Rate (IDR) optimal peaks, generated from the ENCODE pipeline, were obtained for each cell type and used for downstream analyses.
EBV type 1-specific peaks, EBV type 2-specific peaks, and shared peaks were identified using bedtools commands on IDR optimal peaks
Assembly: hg19 (GRCh37)
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format. Peaks are filtered based on q-value and contain only those with a q-value < 0.01
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10
|
| |
|
| Submission date |
Oct 23, 2023 |
| Last update date |
Mar 12, 2024 |
| 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) |
| GSE246060 |
Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome (ChIP-Seq) |
| GSE246062 |
Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome |
|
| Relations |
| BioSample |
SAMN37932662 |
| SRA |
SRX22183925 |
