|
| Status |
Public on Mar 12, 2024 |
| Title |
ATAC-seq: MutuIII Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
MutuIII
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MutuIII
virus type: EBV1
virus strain: Mutu
|
| Growth protocol |
The AG876, Jiyoye, GM12878, and MutuIII 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 |
Transposase Tn5 with sequencing adapter sequences was used to cut the accessible DNA as detailed in Buenrostro et al. 2015
The resulting accessible DNA sequences were isolated, and libraries were prepared from 50,000 cells from each cell line using the OMNI ATAC protocol as detailed in Corces et al 2017
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality control of raw sequencing reads was performed using the DNA Accessibility Pipeline v2.2.0 from the ENCODE Project.
ATAC-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)
Peaks were called using the default parameters of MACS2 (q < 0.01).
Irreproducibility Discovery Rate (IDR) optimal peaks, generated from the ENCODE pipeline, were obtained for each cell type and used for downstream analyses.
Assembly: hg19
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 |
GPL18573 |
| Series (2) |
| GSE246059 |
Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome (ATAC-Seq) |
| GSE246062 |
Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome |
|
| Relations |
| BioSample |
SAMN37932414 |
| SRA |
SRX22185152 |
