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| Status |
Public on Jun 30, 2024 |
| Title |
SCC7-IP |
| Sample type |
SRA |
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| Source name |
SCC7
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| Organism |
Mus |
| Characteristics |
cell line: SCC7
cell type: cancer cell
chip antibody: Stat1 CST, #14994
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| Growth protocol |
DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The tissue/cell was fixed in 1% formaldehyde for 10 min at room temperature by a vacuum pump, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The tissue was then collected and frozen in liquid nitrogen, and grinded by tissue lyser. The grinded powder was treated with lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-STAT1 antibody（Cell Signaling Technology #14994）and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively. The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Mus using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
bigWig files were generated using deepTools.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: bigWig
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| Submission date |
Mar 31, 2023 |
| Last update date |
Jun 30, 2024 |
| Contact name |
An Song |
| E-mail(s) |
annsong@whu.edu.cn
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| Organization name |
Wuhan University
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| Street address |
Luoyu Road 237
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| City |
Wuhan |
| ZIP/Postal code |
430000 |
| Country |
China |
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| Platform ID |
GPL31136 |
| Series (2) |
| GSE228677 |
Glutamine inhibition combined with CD47 blockade enhances radiotherapy-induced ferroptosis in head and neck squamous cell carcinoma [ChIP-Seq Stat1] |
| GSE228679 |
Glutamine inhibition combined with CD47 blockade enhances radiotherapy-induced ferroptosis in head and neck squamous cell carcinoma |
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| Relations |
| BioSample |
SAMN34031488 |
| SRA |
SRX19839827 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7134850_stat1_IP.bw |
164.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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