|
| Status |
Public on Jan 05, 2016 |
| Title |
EBNA3A_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblast Cell Lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Epstein Barr Virus transformed Lymphoblast Cell Line
genotype/variation: expressing HA tagged EBNA3A protein
chip antibody: HA-probe Antibody F-7 (sc-7392; Santa Cruz)
|
| Treatment protocol |
Cells were fixed with 1% formaldehyde. After wash with twice PBS, the cells were lyzed in ChIP lysis buffer. Lysates were sonicated and cleared by centrifugation. HA antibody F-7 (sc-7392; Santa Cruz) was incubated with the lysate overnight at 4ºC.
|
| Growth protocol |
Cells were grown in RPMI media supplemented witth 10%fetal bovine serum, penicillin and streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein A/G magnetic beads was used to capture the protein DNA complexed. The eluted protein-DNA complexes were reverse crosslinked and DNA was purified by a QIAquick PCR purification kit (28706; Qiagen).
Libraries were prepared using PrepX BeadX kit from IntegenX. Briefly, DNA was end-repaired. 3' A base was added and ligated to adaptors. After PCR amplification, DNA was purified and analyzed with Illumina HiSeq.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed by the Harvard Medical School Biopolymer facility as per Illumina recommendations
ChIP-seq reads were aligned to the human hg19 genome assembly using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml)
peaks were called using MOSAiCS (MOdel-based one and two Sample Analysis and inference for ChIP-Seq Data) controlling the false discovery rate (FDR) at 0.05.
Genome_build: hg19 and V01555.2
Supplementary_files_format_and_content: wig files were generated using MOSAiCS; Scores represent read counts
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Johannsen |
| E-mail(s) |
ejohannsen@medicine.wisc.edu
|
| Organization name |
UW-Madison
|
| Department |
Department of Medicine
|
| Street address |
1111 Highland Ave
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE76166 |
EBNA3 proteins regulate EBNA2 binding to distinct RBPJ genomic sites |
|
| Relations |
| BioSample |
SAMN04351193 |
| SRA |
SRX1491920 |
