|
| Status |
Public on Jan 06, 2012 |
| Title |
IgG_1_BCBL1_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
BCBL1 Pleural Effusion Lymphoma (PEL)cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BCBL1
genotype/variation: KSHV positive PEL
chip-antibody: purified IgG
|
| Treatment protocol |
No treatment
|
| Growth protocol |
10% FBS in RPMI with antibiotics
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina Library Preparation Protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
BCBL1 cells per IP with IgG control antibody
|
| Data processing |
Tag_Lana_1_ChIP-Seq_hg18_align_IgG.bed; genome build: hg18
Alignment: Alignment was performed using BOWTIE
Solexa ChIP-Seq experiments were performed with 2x106 BCLB1 cells per IP with either LANA monoclonal antibody or control mouse IgG. BCBL1cells are KSHV positive human Pleural Effusion Lymphoma (PEL) cell line. For Peak calling, A combination of fold ratio and Poisson model for the tag distribution was used to define peaks as follows: (i) Identification of genomic regions (of length 1000bp) enriched with ChIP-seq sequence tags using fold ratio – A genomic region is considered as sequence enriched if the fold ratio, calculated using number of reads normalized to the total reads within that region in ChIP (antibody treatment) sample divided by the number of reads normalized to the total reads in control sample (IgG control) in the same region, is higher than the given cutoff. Nearby enriched regions were merged to make broader enriched genomic regions. A cutoff of 3 was applied to find the initial genomic regions of enrichment at this stage. (ii) Creating the read overlapping profile for each identified region from step 1, by extending the sequence reads from the 5’ end to the 3’ end of the reads up to 300 bps (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol) for the experiment sample. (iii) Peak identification, by using Poisson model – by counting the number of overlapped reads at each nucleotide position and defining the genomic position with the highest number as the peak position within the significant region. Finally, only those genomic regions that have fold ratio > 10 and peak score > 8 and p value < 0.001 (as determined by Poisson background model) are considered as statistically significant. Peak score is calculated as the average value of raw counts within a given region of significant fold enrichment relative to control IgG levels. The average is measured for overlapping tags at every base after extending the tags to their average tag length within the significant region.
|
| |
|
| Submission date |
Jan 05, 2012 |
| 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) |
| GSE34890 |
Identification of Host-Chromosome Binding Sites and Candidate Gene Targets for KSHV LANA |
|
| Relations |
| SRA |
SRX114607 |
| BioSample |
SAMN00769957 |
