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| Status |
Public on Nov 06, 2024 |
| Title |
Cal27-CSC, ATAC-seq |
| Sample type |
SRA |
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| Source name |
Cal27
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Cal27
cell type: Head and neck squamous cell carcinoma
genotype: CSC
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cal27 cells (~1×107) in a logarithmic growth phase with monolayer growth were washed and collected. All samples were fixed with 1% formaldehyde at room temperature for 15 min, followed by 0.125 M glycine treatment for 5 min. The sample was then pelleted, washed and re-suspended in ChIP lysis buffer (25 mM Tris-HCl pH 7.5, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS, 1×Proteinase Inhibitor Cocktail). Then, samples were sonicated by Bioruptor® Plus sonication device (Shearing condition: 20 cycles on cooling condition, 30 seconds ON, 30 seconds OFF), immunoprecipitated with antibody against H3K27ac, BRD4, EP300, SOX2, SMAD3 or Rabbit IgG on ChIP-Grade Protein G Agarose Beads (#9007, Cell Signaling Technology, USA) and purified by Universal DNA Purification Kit (#DP214, TIANGEN Biotech, China).
The ChIP-Seq library was prepared using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (#E7645L, New England Biolabs, USA) according to the manufacturer’s instructions.
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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 ATAC-seq reads were trimmed using Trimmomatic (version 0.39).
Trimmed seuqence reads were aligned using Bowtie2 algorithm (version 2.5.2) to the human reference genome hg19/GRCh37 using the following parameters: -t -p 36 --local --very-sensitive-local --no-discordant --no-mixed.
BAM format data were sorted and indexed with SAMtools (version 1.18).
Peaks calling were utilization the MACS2 (version 2.2.9) algorithm using the following parameters: -g hs -B -f BAM --shift 100 --extsize 200 --SPMR -q 0.01. chrM reads were removed.
Pileup signal (.bed files) were converted to binary big-wig files (.bw file) and Reads Per Kilobase per Million mapped reads (RPKM) normalized by DeepTools (version 3.5.4) using bamCoverage command.
Assembly: hg19
Supplementary files format and content: BigWig, narrowPeak
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| Submission date |
Aug 16, 2024 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Jin Li |
| E-mail(s) |
lijin_dental@njmu.edu.cn
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| Phone |
+86 85031886
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| Organization name |
Nanjing Medical University
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| Department |
OMFS
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| Street address |
140, Hanzhong Road
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| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE274994 |
Super-enhancer driven LIF/LIFR-STAT3-SOX2 regulatory feedback loop promotes cancer stemness in head and neck squamous cell carcinoma (ATAC-seq) |
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| Relations |
| BioSample |
SAMN43223159 |
| SRA |
SRX25734217 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8464063_Cal27csc_ATAC_hg19_RPKM.bw |
21.0 Mb |
(ftp)(http) |
BW |
| GSM8464063_Cal27csc_ATAC_peaks.narrowPeak.gz |
724.3 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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