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Series GSE232265 Query DataSets for GSE232265
Status Public on Feb 03, 2025
Title Effect of MS-275 and CXD101 on open chromatin regions of M-MDSCs [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary To elucidate the molecular mechanisms of HDAC1-3 inhibitors in inhibiting M-MDSCs, ATAC-seq analysis of M-MDSCs isolated from Hepa 1-6 tumor-bearing mice treated with MS-275 or CXD101 were performed.
 
Overall design M-MDSCs (CD11b+Ly-6ChiLy-6G-) were sorted by JSAN (KS-Techno, Japan) from tumor isolated. ATAC-seq libraries were prepared using ATAC-seq Kit (Active Motif, USA) according to the manufacturer’s protocol. Briefly, 1 × 105 M-MDSCs were lysed with ATAC lysis buffer and nuclei were isolated by centrifugation at 500 × g, 4°C for 10 min. Nuclei were then suspended in 50 µL of Tagmentation Master Mix and incubated at 37°C for 30 min with shaking. DNA was purified using DNA purification column and PCR amplification was performed for 10 cycles to introduce sequencing adapters to open chromatin regions. Library DNA was finally purified using Solid Phase Reversible Immobilization beads. Molecular weight was checked and libraries were quantified using Bioanalyzer and submitted for NGS analysis.
 
Contributor(s) Xie Z, Okuzaki D, Tachibana M
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Submission date May 11, 2023
Last update date Feb 03, 2025
Contact name Daisuke Motooka
E-mail(s) dry_team@ngs.gen-info.osaka-u.ac.jp
Organization name NGS core facility, Research Institute for Microbial Diseases, Osaka University
Street address 3-1, Yamadaoka
City Suita
State/province Osaka
ZIP/Postal code 5650871
Country Japan
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (6)
GSM7324768 Vehicle_M1, ATACseq
GSM7324769 Vehicle_M2, ATACseq
GSM7324770 MS275_M1, ATACseq
This SubSeries is part of SuperSeries:
GSE232268 Effect of MS-275 and CXD101 on MDSCs
Relations
BioProject PRJNA971504

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Supplementary file Size Download File type/resource
GSE232265_CXD101_M1_CXD101_M2_vs_MS275_M1_MS275_M2_peaks.narrowPeak.gz 205 b (ftp)(http) NARROWPEAK
GSE232265_CXD101_M1_CXD101_M2_vs_Vehicle_M1_Vehicle_M2_peaks.narrowPeak.gz 7.9 Kb (ftp)(http) NARROWPEAK
GSE232265_MS275_M1_MS275_M2_vs_CXD101_M1_CXD101_M2_peaks.narrowPeak.gz 44.1 Kb (ftp)(http) NARROWPEAK
GSE232265_MS275_M1_MS275_M2_vs_Vehicle_M1_Vehicle_M2_peaks.narrowPeak.gz 213.2 Kb (ftp)(http) NARROWPEAK
GSE232265_Vehicle_M1_Vehicle_M2_vs_CXD101_M1_CXD101_M2_peaks.narrowPeak.gz 18.3 Kb (ftp)(http) NARROWPEAK
GSE232265_Vehicle_M1_Vehicle_M2_vs_MS275_M1_MS275_M2_peaks.narrowPeak.gz 17.5 Kb (ftp)(http) NARROWPEAK
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Raw data are available in SRA
Processed data are available on Series record

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