|
| Status |
Public on Dec 31, 2020 |
| Title |
H3K4me3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Erythrocyte cell
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Lohmann
cell type: G0 phase Immature erythrocyte cells
strain: White leghorn
chip antibody: H3K4me3 (abcam:8580,lot:188955-1)
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| 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 libraries for H3K4me3 and H3K27ac antibodies (Abcam) were prepared according to the 5500 SOLiD fragment library protocol (Life technologies). 5 ug of sheared genomic DNA and 30 ng of ChIP DNA were end-repaired and size selected (100-250bp), followed by dA tailing, ligation of SOLiD barcodes and library PCR amplification. Libraries were subjected to emulsion PCR (ePCR) and loaded on the flowchip for 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
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: gal3
Supplementary_files_format_and_content: peaks.bigwig
|
| |
|
| Submission date |
Mar 26, 2019 |
| 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) |
| GSE128864 |
Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [ChIP-seq] |
| GSE141015 |
Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes |
|
| Relations |
| BioSample |
SAMN11257970 |
| SRA |
SRX5576714 |
