|
| Status |
Public on Oct 05, 2022 |
| Title |
LMH cells, overexpression of chicken p53 with flag, Input1 |
| Sample type |
SRA |
| |
|
| Source name |
LMH
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: LMH
cell type: liver cells
genotype: p53 overexpression
chip antibody: none
|
| Growth protocol |
LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine. Cell cultures were incubated at 37°C/5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
LMH cells were fixed in 1% formaldehyde for 10 min and then with 0.125 M glycine. Each ChIP experiment was performed with sheared chromatin samples and indicated antibody. The immunoprecipitated DNA was purified using a QIAquick PCR Purification Kit (28106, QIAGEN, Valencia, CA).
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq2 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the Gallus_gallus-4.0 genome using Bowtie version 2.1.0. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01. bigWig files were generated using the genomicRanges R package.
Assembly: Gallus_gallus-4.0
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Apr 07, 2022 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Hai Li |
| E-mail(s) |
lihai@xjtu.edu.cn
|
| Organization name |
Xi'an Jiaotong University
|
| Department |
Department of Pathogenic Microbiology and Immunology
|
| Street address |
No.76 Yanta West Road
|
| City |
Xi'an |
| ZIP/Postal code |
710061 |
| Country |
China |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE200405 |
Exploration of the genome-wide DNA binding of chicken p53 in LMH cells |
|
| Relations |
| BioSample |
SAMN27403522 |
| SRA |
SRX14776047 |
