|
| Status |
Public on Dec 16, 2015 |
| Title |
EBF1 CHIP-seq in LCL |
| Sample type |
SRA |
| |
|
| Source name |
LCL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LCL
cell type: EBV positive B-cells
chip antibody: EBF1
chip antibody vendor: EMD Millipore
chip antibody cat. #: AB10523
chip antibody lot #: Q2062041
|
| Treatment protocol |
Cells were maintained and isolated in logarihmic growth phase for ChIP-assays
|
| Growth protocol |
EBV positive B-cell (Mutu I, LCL) were grown in RPMI with 10% FBS and Glutamax
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq protocol is as described previously (Lu et al, 2010 Virology journal 7, 262).
Library was constructed using the TruSeq ChIP Sample Prep kit (Illumina) according to manufacturers instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
WST_LCL_EBF1
|
| 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 to human genome hg19 using bowtie using "-v 2 -m 1 -best -strata" option on unique reads
Peak calling was done with homer (v1.0) software
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains Homer peak calling output
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| 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 (2) |
| GSE75503 |
Combinatorial Control of RBP-jk and EBF1 Chromosome Occupancy induced by viral co-activator EBNA2 [ChIP-seq] |
| GSE75504 |
Combinatorial Control of RBP-jk and EBF1 Chromosome Occupancy induced by viral co-activator EBNA2 |
|
| Relations |
| BioSample |
SAMN04301874 |
| SRA |
SRX1456193 |
