|
| Status |
Public on Oct 08, 2022 |
| Title |
Control_1_H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: adeno carcinoma
tissue source: lung tissue
chip antibody: H3K27ac (MABI0309, MAB Institute)
treatment: Control siRNA
|
| Treatment protocol |
A549 cells were transfected with control siRNA or CEBPB siRNA-1, CEBPB siRNA-2. 24hrs after transfection, the culture medium was replaced with fresh DMEM supplemented with 10% FBS and penicillin/streptomycin. After additional 24 hrs, cell were harvested for chromatin precipitation.
|
| Growth protocol |
A549 cells were incubated in the DMEM supplemented with 10% FBS and penicillin/streptomycin.The cells were cultured at 37oC under 5% CO2 and saturated humidity in 20% oxygen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were prepared from sonicated nuclei, and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEW ENGLAND BioLabs). The libraries were further purified and size-selected using an AMPure XP Kit (Beckman Coulter) and were quantified using a quantitative MiSeq (qMiSeq) method. Optimally diluted libraries were sequenced on a HiSeq2500 (Illumina) to generate 101-base single-end reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequenced reads were mapped into hg19 using BWA 0.7.17.
Duplicated reads were marked by using SAMBLASTER version 0.1.26.
Duplicates and reads with mapping quality less than 6 were removed using SAMTools version 1.7.0.
PyMaSC version 0.3.2 was used to estimate a mean fragment length for each ChIPped sample.
Peaks were called with MACS2 version 2.2.7.1 with the following parameters: --SPMR --nomodel --extsize <mean_fragment_size>
Genome_build: hg19
Supplementary_files_format_and_content: Peak files (narrowPeak format) were generated by MACS2.
Supplementary_files_format_and_content: BigWig files were converted from bedGraph files by the bedGraphToBigWig command. They include the normalized (per 1M reads) depth of treat DNA fragment pileup calculated by MACS2.
|
| |
|
| Submission date |
Oct 19, 2021 |
| Last update date |
Oct 08, 2022 |
| Contact name |
Hozumi Motohashi |
| E-mail(s) |
hozumi.motohashi.a7@tohoku.ac.jp
|
| Phone |
81-22-717-8089
|
| Organization name |
Tohoku University
|
| Department |
Medical Biochemistry
|
| Street address |
2-1 Seiryo-machi, Aoba-ku
|
| City |
Sendai |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE186186 |
CEBPB-dependent enhancer formation in NRF2-activated non-small cell lung cancer cell line A549 [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN22416933 |
| SRA |
SRX12695685 |
