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| Status |
Public on Jun 17, 2024 |
| Title |
Periosteal Cells, Lys27, Chip |
| Sample type |
SRA |
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| Source name |
Periosteum
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| Organism |
Mus musculus |
| Characteristics |
tissue: Periosteum
strain: C57BL/6J
chip antibody: Acetyl-Histone H3 (Lys27) (CST,#8173s)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Primary periosteal cells (Ter119-CD45-CD31-PDPN+ PDGFRα+ cells) were isolated from the tumor-excised calvarial tissues from the scratch-negative groups one week after the implantation of HNM007 cell. Chromatin immunoprecipitation on 100,000 periosteal cells was performed with CUT&RUN Assay Kit (CST, #86652) using antibodies to acetylated histone H3 Lys27 (H3K27ac) (CST,#8173s), H3K4me3 (CST,#9751) and HIF-1α (CST,#36169). Illumina sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat No. 7645) according to the manufacturer's instructions. Barcoded libraries were run on the NovaSeq 6000 in a PE150 run, and an average of 40 million paired reads were generated per sample.
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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 |
ChIP-seq data were processed using Galaxy server https://usegalaxy.org. (The Galaxy Community. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345-W351, doi:10.1093/nar/gkac247). For mapping and visualization, paired-end FASTQ reads were mapped to mouse genome mm10 using Bowtie2 (v 2.5.0) with default filtering criteria. Resulted BAM files were converted to BED format using bedtools (v2.30.0). Peak calling of the Lys4 ChIP, Lys27 and HIF-1α and its corresponding Input was performed using MACS2 (v 2.2.9.1) with the --nomodel option and a p-value cutoff of 0.01 with the narrow peak option was used. The generated BedGraph files were converted to Bigwig format and visualized using IGV v2.13.0.
Assembly: Mouse genome build GRCm38/mm10
Supplementary files format and content: bigwig
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| Submission date |
Feb 21, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Masayuki Tsukasaki |
| E-mail(s) |
tsuka-im@m.u-tokyo.ac.jp
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| Organization name |
The University of Tokyo
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| Department |
Department of Immunology Graduate School of Medicine and Faculty of Medicine
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| Street address |
7-3-1, Hongo
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| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE256307 |
ChIP–seq on periosteal cells derived from the pre-invasive group using antibodies to acetylated histone H3 Lys27 (H3K27ac), H3K4me3 and HIF-1α |
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| Relations |
| BioSample |
SAMN40026589 |
| SRA |
SRX23691462 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8093388_Lys27.bigwig |
342.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
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