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| Status |
Public on Mar 15, 2019 |
| Title |
Fayoumi biological replicate1 individual injected with avian inluenza virus [FI1_A] |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Gallus gallus |
| Characteristics |
breed: Fayoumi M43
age: 3 weeks
tissue: Lung
treatment: Avian influenza virus infection
chicken identifier: F1
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| Treatment protocol |
Two Leghorn and two Fayoumi birds were euthanized at 3 weeks and injected with avian influenza virus, and lungs were harvested. The animal experiment was performed according to the guidelines approved by the Institutional Animal Care and Use Committee, Texas A&M University.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from lung tissue was isolated by phenol-chloroform extraction.
Libraries were prepared as below. Five μg DNA was sonicated to produce 200-400 bp fragments, followed by end repair with a nucleotide triphosphate mix free of dCTP. Cytosine methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA according to the manufacturer’s instructions for genomic DNA library construction. Adapter-ligated DNA with the length of 320-500 bp was isolated by 2% agarose gel electrophoresis, and sodium bisulfite conversion was performed on it using the MethylEasy Xceed kit (Human Genetic Signatures, NSW, Australia) was used according to the manufacturer’s instructions. The 300 ng of bisulfite-converted, adapter-ligated DNA molecules were enriched by 14 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive Pfu TurboCx Hotstart DNA polymerase (Stratagene), 5 μL of 10× Pfu Turbo reaction buffer, 25 μM dNTPs, 1 μL of Primer 1.1, and 1 μL of Primer 2.1 (50 μL final). The thermocycling parameters were as follows: 98°C for 2 min, followed by 4 cycles of 98°C for 15 s, 60°C for 30 s, and 72°C for 1 min, ending with incubation at 72°C for 10 min. The reaction products were purified using the MinElute PCR purification kit (Qiagen, Valencia, CA) and then separated by 2% agarose gel electrophoresis and purified by the MinElute gel purification kit (Qiagen, Valencia, CA). DNA library prepared above was sequenced using the Illumina Genome Analyzer II (GA II) according to the manufacturer’s instructions. Each sample had two technical replicates.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
FI1_A
MethylC-seq
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| Data processing |
Sequenced reads were aligned to the galGal4 genome assembly using Bismark version 0.13.0 with the following configurations: -N 1 -L 20 --bowtie2 --bam -1 -2 -p -o.
Extracted CG methylation rates were generated by Bismark_methylation_extractor subprogram.
Single site methylation rate was used to identify the differential methylation sites and differential methylation regions, and then false discovery rate (FDR) was used to correct it (p = 0.01).
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: *_bismark_bt2_pe.bismark.zero.cov: Tab-delimited text files include chromosome, position of methylcytosines which were identified for each chicken line (LI represents Leghorn chicken injected with AIV; FI represents Fayoumi chicken injected with AIV). The files contain <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>.
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| Submission date |
Mar 14, 2019 |
| Last update date |
Mar 16, 2019 |
| Contact name |
Jing An |
| Organization name |
Universite Paris Saclay
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| Street address |
630 Rue Noetzlin
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| City |
Paris |
| ZIP/Postal code |
91190 |
| Country |
France |
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| Platform ID |
GPL9385 |
| Series (1) |
| GSE128053 |
A homeostasis hypothesis of avian influenza resistance in chickens |
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| Relations |
| BioSample |
SAMN11127692 |
| SRA |
SRX5523262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3671356_FI1_A_read1_4L.fq_bismark_bt2_pe.bismark.zero.cov.gz |
125.8 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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