|
| Status |
Public on Nov 09, 2023 |
| Title |
A549, H3K27me3, ChIP, Biol Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
A549
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: Human lung carcinoma
genotype: WT
treatment: None
antibody: H3K27me3 (Abcam, ab6002)
|
| Treatment protocol |
For doxycyline treated cells, doxycyline was added to cell medium a final concentration of 1 μg/mL. Cells were fixed with formaldehyde 48 hours after doxycycline induction.
|
| Growth protocol |
Ham's F-12K (Kaighn's), 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with formaldehyde (1% final concentration) for 10 minutes at room temperature. Crosslinking was quenched with glycine (0.125M final concentration) for 5 minutes ar room temperature. After cell and nuclei lysis, chromatin was fragmented in Diagenode Pico with a circulating water bath at 4°C using the Shear and Go Easy Mode setting for 3 cycles (30 seconds on followed by 30 seconds off).
Sequencing library was constructed by NEBNext ultra II DNA library prep kit (NEB E7103L). 50 million paired-end 50bp reads were obtained for each ChIP and input sample using a NextSeq 2000 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using DRAGEN BCL Convert (v3.8.4).
Paired-end reads were filtered using fastp (Version 0.23.2) according to default settings.
Filtered reads were aligned to the human reference genome (hg38) using BWA-MEM2 (Version 2.2.1)
Resulting BAM files were filtered for MAPQ scores > 20 using SAMtools (Version 1.8)
Read coverage (bigwig file) was obtained separately for input and ChIP samples using deepTools “bamCoverage”, with a bin size of 10 bp (Version 3.5.1). In this step, blacklisted regions were removed (hg38 Version 2, https://doi.org/10.1038/s41598-019-45839-z)
ChIP peaks were called using MACS2 callpeak with the default settings (Version 2.1.1.20160309).
Assembly: hg38
Supplementary files format and content: bigwig for ChIP and input samples
Supplementary files format and content: bed only for ChIP samples
|
| |
|
| Submission date |
Nov 09, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Lu Bai |
| E-mail(s) |
[email protected]
|
| Organization name |
Penn State University
|
| Street address |
406 South Frear Building
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE247412 |
Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 [ChIP-seq] |
| GSE247432 |
Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 |
|
| Relations |
| BioSample |
SAMN38194699 |
| SRA |
SRX22478439 |
