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Sample GSM829546 Query DataSets for GSM829546
Status Public on Jan 01, 2013
Title 63_inf.H3K27me3
Sample type SRA
 
Source name thymus tissue
Organism Gallus gallus
Characteristics strain: line 63
tissue: thymus
infection status: infected
ChIP: H3K27me3
Treatment protocol The chickens were injected intra-abdominally with a partially attenuated very strong strain of MDV (648A passage 40, vv+) at 5 days after hatch with a viral dosage of 500 plaque-forming units (PFU). Chickens were terminated at 10dpi to collect thymus tissues. All procedures followed the standard animal ethics and use guidelines of ADOL.
Growth protocol Two specific-pathogen-free inbred lines of White Leghorn either resistant (L63) or susceptible (L72) to MD were hatched, reared and maintained in Avian Disease and Oncology Laboratory (ADOL, Michigan, USDA).
Extracted molecule genomic DNA
Extraction protocol ChIP was carried out using thymus samples from MDV infected and controls birds as follows: About 30mg thymus samples from three individuals were cut into small pieces (1 mm3) and digested with MNase to obtain mononucleosomes. PNK and Klenow enzymes (NBE, Ipswich, MA, USA) were used to repair the ChIP DNA ends pulled down by the specific antibody. A 3′ A was then added using Taq polymerase for adaptor ligation. A pair of Solexa adaptors (Illumina, USA) was ligated to the repaired ends. Seventeen cycles of PCR was performed on ChIP DNA using the adaptor primers and fragments with a length of about 190 bp (mononucleosome + adaptors) were isolated from agarose gel. Subsequently, cluster generation and sequencing analysis using the purified DNA was performed on the Solexa 1G Genome Analyzer (Illumina, USA) following manufacturer protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Alignment: Sequence reads were aligned to the May 2006 version of the chicken genome (galGal3) using Maq version 0.7.1 (Li et al. 2008). A valid alignment could have a maximum of two mismatches and if a read aligned equally well to multiple places in the genome, one was chosen at random. Redundant reads were removed before further analysis to avoid amplification bias. Read counts were summarized using non-overlapping windows of 200 bp for visualization.
Peak calling: Summarized read counts were subjected to peak calling with SICER (Zang et al. 2009). The source code was modified to include support for the chicken genome. Fragment length was specified to be about 190 bp as estimated from our ChIP-Seq experiments. A window size of 200 bp (default) and gap size of 400 bp was used for the analysis. The E-value for estimating significant peaks was set to 100.
 
Submission date Nov 08, 2011
Last update date May 15, 2019
Contact name Apratim Mitra
E-mail(s) apratim.mitra@nih.gov
Phone 3014020676
Organization name NICHD
Department Division of Developmental Biology
Lab Section on Genomic Imprinting
Street address 6 Center Dr Building 6B Room 2B206
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL13797
Series (1)
GSE33541 Marek's Disease Virus Infection Induces Differential Chromatin Marks and Tissue-specific effects in inbred chicken lines
Relations
SRA SRX104945
BioSample SAMN00750651

Supplementary file Size Download File type/resource
GSM829546_out.T_K27_L63_inf_s_3_sequence.bed.gz 46.3 Mb (ftp)(http) BED
GSM829546_out.T_K27_L63_inf_sequence.all-W200-G400.probscoreisland.gz 278.9 Kb (ftp)(http) PROBSCOREISLAND
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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