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| Status |
Public on Jun 28, 2023 |
| Title |
ChIP_Seq analysis in cultured mTSC cells with or without Dox |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To detect the direct target genes of H4K20me1, H4K20me3, and H3K4me3 in mTSCs, mTSCs with or without Dox are collected and subjected to ChIP-Seq. After aligned to mouse mm10 by HISAT2, peaks are called by MACS2. Our results show that methylation of H4K20 mediated by Pr-set7 as the key regulator of mTSCs, indicating the essential role of Pr-set7. This ChIP-Seq data provides fundamental information for our further physiological study of Pr-set7.
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| Overall design |
ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x106 TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.
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| Contributor(s) |
Lu J |
| Citation(s) |
37307441 |
| Submission date |
Feb 06, 2022 |
| Last update date |
Jun 29, 2023 |
| Contact name |
Jinhua Lu |
| E-mail(s) |
jinhua888@126.com
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| Organization name |
Xiamen University
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| Street address |
No. 4221, Xiangan Road, Xiangan District, Xiamen city
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| City |
Xiamen |
| ZIP/Postal code |
361000 |
| Country |
China |
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| Platforms (1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA803922 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE196222_RAW.tar |
524.4 Mb |
(http)(custom) |
TAR (of TDF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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