|
| Status |
Public on Dec 16, 2015 |
| Title |
EBNA1 CHIP-seq in MutuI |
| Sample type |
SRA |
| |
|
| Source name |
EBNA1 CHIP-seq in MutuI
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MutuI
cell type: EBV positive B-cell
chip antibody: EBNA1
|
| Treatment protocol |
maintained and isolated in logarihmic growth phase
Cells were maintained and isolated in logarihmic growth phase for ChIP-assays. RNA Seq analysis was performed with LCL cells transduced with either pLKO.1 shControl or shEBNA1 lentivirus after 5 days of puromycin selection.
|
| Growth protocol |
EBV positive B-cell (Raji, Mutu I, LCL) were grown in RPMI with 10% FBS and Glutamax. EBV positive NPC-line C666-1 was grown in DMEM with 10% FBS and Glutamax.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lu et al, 2010 Virology journal 7, 262
The EBNA1 antibody is a rabbit polyclonal antibody raised to full length EBNA1(lacking Gly-Ala repeats). The rabbit injections and bleeds were provided by Pocono Rabbit Farm. Reactive serum was affinity purified against full length EBNA1, and 10 ug of affinity purified antibody was used for 50 million cells for each ChIP experiment.
TruSeq ChIP Sample Prep kit
ChIP-Seq protocol is as described previously (Lu et al, 2010 Virology journal 7, 262). Total RNA was isolated for RNA-Seq using Trizol reagent.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
CHIP.MutuI.EBNA1
|
| Data processing |
All chip-seq files were generated by Illumina GA II and base calling was done with CASAVA 1.5
Chip-seq files were aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with homer (v1.0) software with -center -o, -fdr 0.2
RNA-Seq data analyzing was done with rsem(ver. 1.2.3) and Hg19 genome with UCSC known gene set.
edgeR was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains Homer peak calling output while expression file contains the edgeR output; details in the 'readme.txt'
|
| |
|
| Submission date |
Oct 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
[email protected]
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE73887 |
Identification of MEF2B, EBF1, and IL6R as chromosome bound targets of EBNA1 essential for EBV infected B-lymphocyte survival |
|
| Relations |
| BioSample |
SAMN04158407 |
| SRA |
SRX1322298 |
