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| Status |
Public on Apr 17, 2015 |
| Title |
bursa_K4_L63_non_5_2 |
| Sample type |
SRA |
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| Source name |
bursa tissue
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| Organism |
Gallus gallus |
| Characteristics |
histone mark: H3K4me3
chicken line: L63
days post infection: 5
condition: control
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| Treatment protocol |
Eight chickens from each line were injected intra-abdominally with a partially attenuated very virulent plus strain of MDV (648A passage 40) at 14 days after hatch with a viral dosage of 500 plaque-forming units (PFU). Another eight chickens were not infected as age-matched controls. Infected and control chickens (n=4) from both lines were terminated at 5 or 10dpi to collect bursa tissues. All procedures followed the standard animal ethics and use guidelines of ADOL.
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| 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).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 30 mg bursa samples were digested with micrococcal nuclease to obtain mononucleosomes.
MNase digestion was followed by end-repair with PNK and Klenow enzymes (NBE, Ipswich, MA, USA) and ChIP with the specific antibody (H3K4me3: Millipore, Cat. #17-614; H3K27me3: Abcam, Cat. # ab6002). This was followed by addition of 3’ adenine, Illumina adaptor ligation, PCR amplification (17 cycles) and size-selection (~ 150 bp), cluster generation and sequencing on the Illumina Hi-Seq 2000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequence reads were aligned to the chicken genome version galGal3 using bowtie version 0.12.7 (Langmead et al. 2009). Default alignment policies of bowtie were enforced: 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. If multiple r\eads mapped to the same genomic location, only one was kept to avoid amplification bias.
Peak-calling was carried out using the WaveSeq algorithm (Mitra et al. 2012). We used recommended values for parameters: for H3K4me3 data, the mother function was ‘morlet’ and gap size was 2 (400 bp), while for H3K27me3, the mother function was ‘mexican hat’ and gap size was 10. For increased sensitivity for the broad H3K27me3 mark, the p-value threshold was lowered to 0.4.
Genome_build: galGal3
Supplementary_files_format_and_content: bedGraph files were generated using WaveSeqR package (http://r-forge.r-project.org/projects/waveseqr/). Redundant reads were removed and interval size was 200 bp. Scores represent total read count within corresponding genomic interval.
Supplementary_files_format_and_content: Peak files were generated using WaveSeqR. Each row represents one peak with the following information in six columns: chromosome, start, end, read count, p-value, adjusted p-value.
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| Submission date |
Feb 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Apratim Mitra |
| E-mail(s) |
apratim.mitra@nih.gov
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| Phone |
3014020676
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| Organization name |
NICHD
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| Department |
Division of Developmental Biology
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| Lab |
Section on Genomic Imprinting
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| Street address |
6 Center Dr Building 6B Room 2B206
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL16133 |
| Series (1) |
| GSE65961 |
Histone modifications induced by MDV infection at early cytolytic and latency phases |
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| Relations |
| BioSample |
SAMN03350212 |
| SRA |
SRX878703 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1611734_bursa_K4_L63_non_5_2_waveseq_peaks.txt.gz |
164.7 Kb |
(ftp)(http) |
TXT |
| GSM1611734_out.bursa_K4_L63_non_5_2_align_sorted-W200.bedgraph.gz |
21.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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