|
| Status |
Public on Jan 01, 2016 |
| Title |
H3K4me3ChIPseq of cell sample sD |
| Sample type |
SRA |
| |
|
| Source name |
Erythrocyte cell
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Bovan
develomental stage: G0 phase Immature erythrocyte cells
layer: White leghorn
antibody information: H3K4me3 (abcam:8580,lot:188955-1)
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| 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(%)
|
| |
|
| 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
|
| Organization name |
University of Manitoba
|
| Department |
Biochemistry and Medical Genetics
|
| Street address |
745 Bannatyne Avenue, RM 333A
|
| City |
Winnipeg |
| State/province |
Manitoba |
| ZIP/Postal code |
R3E 0J9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21224 |
| Series (2) |
| GSE75845 |
Genome-wide mapping of H3K4me3 and H3K27ac in chicken immature erythrocyte cells |
| GSE75955 |
The chicken erythrocyte epigenome |
|
| Relations |
| BioSample |
SAMN04327495 |
| SRA |
SRX1472820 |
