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| Status |
Public on Jan 01, 2016 |
| Title |
H3K27ac of cell sample sD (MiSeq) |
| Sample type |
SRA |
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| Source name |
Erythrocyte cell
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| Organism |
Gallus gallus |
| Characteristics |
strain: Bovan
develomental stage: G0 phase Immature erythrocyte cells
layer: White leghorn
antibody information: H3K27ac (abcam 4729, lot 124541)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chicken immature erythrocyte nuclei were treated with 0.5% formaldehyde and chromatin was sheared into 200bp fragments. Immunoprecipitation was performed with respective antibody.
ChIPSeq library preparation was performed according to the NEBNext ChIP-Seq library preparation protocol. 20 ng of ChIP DNA was end-repaired and dA-tailed. Ligation products were size selected and PCR enriched. Libraries were quantified by qPCR,normalized and pulled to 10 nM before sequencing.ChIP DNA and Input libraries were sequenced using the MiSeq platform and v3 sequencing reagents.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Data processing |
XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
Fastq sequences with 76bp generated by Miseq were trimmed off the first 3 bases and the last 2 bases and mapped onto reference genome by bowtie-0.12.8.
ChIPseq workflow of LifeScope was used
Adaptor and barcode sequences were removed
peaks were called using the bed files by MACS1.4 program
peak pvalue cutoff = 1.00e-05
Genome_build: galGal3
Supplementary_files_format_and_content: peaks.xls, chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment FDR(%)
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| Submission date |
Dec 09, 2015 |
| Last update date |
Jan 16, 2023 |
| Contact name |
James Ronald Davie |
| E-mail(s) |
jim.davie@umanitoba.ca
|
| Phone |
2042723174
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| Organization name |
University of Manitoba
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| Department |
Biochemistry and Medical Genetics
|
| Street address |
745 Bannatyne Avenue, RM 333A
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| City |
Winnipeg |
| State/province |
Manitoba |
| ZIP/Postal code |
R3E 0J9 |
| Country |
Canada |
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| Platform ID |
GPL19064 |
| Series (2) |
| GSE75845 |
Genome-wide mapping of H3K4me3 and H3K27ac in chicken immature erythrocyte cells |
| GSE75955 |
The chicken erythrocyte epigenome |
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| Relations |
| BioSample |
SAMN04327490 |
| SRA |
SRX1472823 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1968790_H3K27ac_2.xls.gz |
43.8 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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