|
| Status |
Public on Jan 01, 2013 |
| Title |
72_non.H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
thymus tissue
|
| Organism |
Gallus gallus |
| Characteristics |
strain: line 72
tissue: thymus
infection status: control
ChIP: H3K4me3
|
| 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 |
SRX104948 |
| BioSample |
SAMN00750654 |
