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Sample GSM1404654 Query DataSets for GSM1404654
Status Public on Mar 18, 2015
Title Zta chip
Sample type SRA
 
Source name Akata BL cell line
Organism Homo sapiens
Characteristics pathogen: Epstein-Barr virus
cell line: Akata
cell type: B lymphocytes
acyclovir dose: no acyclovir
antibody: anti-Zta (BZLF1)
antibody manufacturer: Santa Cruz
antibody catalog number: sc-17503
Treatment protocol 0.125% rabbit anti-human IgG anti-IgG was added for 48 hours
Growth protocol RPMI medium supplemented with 10% (v/v) fetal bovine serum, 100units/ml penicillin, 100μg/ml streptomycin and 2mM L-glutamine
Extracted molecule genomic DNA
Extraction protocol Chromatin was fixed by application of 1% (v/v) formaldehyde for 15 min then sonnicated on ice (10 x 10s-pulses; 30% amplitude output on a Branson model 250 Microtip at setting 5 (Sonics Vibacell). The chromatin was pre-cleared with protein A/G-sepharose bead slurry (Sigma) that had been pre-blocked in 0.5% (w/v) fraction V BSA (Sigma) in DPBS. 2% (v/v) of the pre-cleared extract was retained as the input control sample while the remainder was incubated with 10μg of Zta-specific goat antibody (Santa Cruz # sc-17503) or control goat IgG for 1 h at 4oC]. The input control sample and the precipitated DNA were sequentially treated with 0.2μg/ml RNAse A and 0.2μg/ml Proteinase K and the DNA purified.
Sequencing libraries were prepared using 10ng of the input and ChIP DNA using a ChIP-Seq sample preparation kit (Illumina) following the manufacturer’s protocol, except that the library (150-350bp fragments) was purified from the gel after PCR-amplification. The DNA fragments were separated on a 2% agarose gel in TAE buffer, visualized using SYBR-safe stain and 150-300bp fragments were excised and purified using a gel extraction kit (Qiagen).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Zta ChIP
with 0.125% rabbit anti-human IgG anti-IgG added 48 hours
Data processing Initial processing of sequencing images was carried out using the CASAVA pipeline. Base calling, and quality control statistics were performed using GOAT and Bustard modules.
Sequence reads were aligned to the hg19 release of the human genome with ELAND.
Bigwig files were generated by calculating tag density in 10-bp windows, normalizing per million total reads and subtracting the input signals using in-house R scripts.
Peak calling (p<10−7) was performed from a merged Bed file generated from the two ChIP datasets using MACS, with a merged input Bed file acting as background.
Genome_build: hg19
Supplementary_files_format_and_content: MACS output
 
Submission date Jun 05, 2014
Last update date May 15, 2019
Contact name Alison Jane Sinclair
E-mail(s) a.j.sinclair@sussex.ac.uk
Organization name University of Sussex
Department School of Life Sciences
Lab Biochemistry and Bioscience
Street address University of Sussex
City Brighton
State/province E. Sussex
ZIP/Postal code BN1 9QG
Country United Kingdom
 
Platform ID GPL10999
Series (2)
GSE58245 Genomic-scale identification of host genes regulated by EBV during lytic cycle [ChIP-Seq]
GSE58246 Genomic-scale identification of host genes regulated by EBV during the lytic cycle
Relations
BioSample SAMN02839410
SRA SRX573000

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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