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| Status |
Public on Aug 28, 2014 |
| Title |
MediumVaccinated1 |
| Sample type |
SRA |
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| Source name |
Trachea scrape
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| Organism |
Gallus gallus |
| Characteristics |
breed: Leghorn
timepoint: 6 days post infection
precipitation mol: MBD2 protein
concentration: Medium elute viral load (3.3 x 103 pfu)
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| Treatment protocol |
After 6 days, the control group received only sterile vaccine diluent (50 μl per nostril and 50 μl per eye, for a total dose of 200 μl per animal) and then allocated in a separated animal room. Later, the vaccine was prepared following the manufacturer’s recommendations and the vaccination was performed in the second group. The procedure was the same as for the control group, excepting for the viral load (3.3 x 103 pfu). The vaccinated birds were placed in an animal isolator in another suite.
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| Growth protocol |
All chickens were obtained from Charles River Laboratories. They consist in ten, 15 day-old White Leghorn chickens that were randomly assigned to groups of five birds each.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from five samples of each group was extracted using the Wizard Genomic DNA purification kit (Promega, A1120)
MethylCap kit (Diagenode, C02020010) was employed to obtain DNA containing methylated CpGs.
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| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Medium elute concentration
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| Data processing |
Sequencing analyses in the Solexa 1G Genome Analyzer (Illumina)
Alignment with Bowtie
The peak-calling step was applied individually for each sample using Model Based Analysis of ChIP-Seq (MACS)
Identification of the Differentially Methylated Regions (DMRs) was accomplished implementing the DiffBind R package.It computes differentially bound sites using affinity data. The set of peaks identified by MACS and the bam files containing aligned reads for each sample, was the input for DiffBind. The program creates a matrix with the consensus peaks; for this case it was obtained with a “minimum overlap” of 2, determined by the number of replications in the experiment. After creating a contrast between conditions and considering concentration as a block effect, DiffBind runs an edgeR analysis, which is an empirical Bayes method. For normalization, the default method TMM (Trimmed Mean of M-values) that subtracts the controls reads and considers the effective library size (reads in peaks), was applied. The threshold utilized was 0.1, for False Discovery Rate (FDR).
For the genomic annotation of the DMRs, the software ChIPpeakAnno was used [60]. ChIPpeakAnno provides information about the overlaps, relative position and distances for the inquired feature. The annotation information was obtained from biomart, using Ensembl 70 in the archive site. Dataset “ggallus_gene_ensembl” corresponds to WASHUC2 (galGal3), the genome used for alignment.
Genome_build: galGal3
Supplementary_files_format_and_content: Sequencing, fastq; alignment, sam; peak calling from MACS, bed; DMR, xls; annotation, xls
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| Submission date |
Apr 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Adrian Carrillo |
| E-mail(s) |
carrillo@umd.edu
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| Organization name |
University of Maryland
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| Department |
Department of Animal and Avian Sciences
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| Lab |
Song's lab
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| Street address |
1413 Animal Sciences Center
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| City |
College Park |
| State/province |
MD |
| ZIP/Postal code |
20742-2311 |
| Country |
USA |
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| Platform ID |
GPL10223 |
| Series (1) |
| GSE56984 |
Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine |
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| Relations |
| BioSample |
SAMN02731773 |
| SRA |
SRX523607 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1372626_MV1_peaks.bed.gz |
426.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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