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| Status |
Public on Apr 18, 2024 |
| Title |
HK1_sgFLI1_Control |
| Sample type |
SRA |
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| Source name |
nasopharynx
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| Organism |
Homo sapiens |
| Characteristics |
tissue: nasopharynx
cell line: HK1
cell type: Nasopharyngeal carcinoma cells
genotype: FLI1 knockout
treatment: Control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysis occurred using a cold lysis buffer comprising 10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, and 0.1% IGEPAL CA-630. Nuclei were promptly spun at 500 × g for 10 minutes at 4℃, with subsequent discarding of the supernatant.
After purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM custom Nextera PCR primers. The PCR conditions involved an initial step at 72°C for 5 minutes, followed by denaturation at 98°C for 30 seconds, and subsequent thermocycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. A final extension step was performed at 72℃ for 5 minutes. The libraries were then purified using a Qiagen PCR cleanup kit, resulting in the final library.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing reads underwent a series of preprocessing steps to obtain high-quality clean reads. This involved removing sequencing adapters, short reads with a length less than 35 bp, and low-quality reads using Trimmomatic v0.3.
FastQC was employed to ensure the quality of the resulting reads. The clean reads were then aligned to the human genome (assembly GRCh38) using the Bowtie2 v2.3.4.1 software. Alignments with low mapping quality scores (MAPQ < 30). were filtered out using samtools.
To further improve data quality, duplicate reads were removed using the picard MarkDuplicates (http://broadinstitute.github.io/picard). For peak detection, the MACS v2.1.2 peak finding algorithm was utilized with a q-value cutoff of 0.05 to identify significant peaks.
To evaluate the reproducibility of the high-throughput experiments, the irreproducible discovery rate (IDR v2.0.2) analysis was performed, and only reproducible peaks with an IDR value of 0.05 or less were retained. Next, the peak sites were annotated to gene features using the ChIPseeker R package.
To detect potential motifs within the identified peaks, the MEME suite (http://meme-suite.org/) was employed. Lastly, differential peaks between two comparison groups were identified using The DiffBind with a q-value cutoff of 0.05.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
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| Submission date |
Nov 15, 2023 |
| Last update date |
Apr 18, 2024 |
| Contact name |
wuguo deng |
| E-mail(s) |
dengwg@sysucc.org.cn
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| Phone |
15627863020
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| Organization name |
Sun yat-sen university
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| Street address |
651 Dongfengdongroad, Guangzhou, Guangdog
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE247895 |
FLI1 promotes IFN-γ-induced kynurenine production to impair anti-tumor immunity (ATAC-Seq) |
| GSE247898 |
FLI1 promotes IFN-γ-induced kynurenine production to impair anti-tumor immunity |
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| Relations |
| BioSample |
SAMN38268916 |
| SRA |
SRX22537801 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7902856_HK1-KO-Control.bw |
156.1 Mb |
(ftp)(http) |
BW |
| GSM7902856_HK1-KO-Control__peaks.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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