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Series GSE248891 Query DataSets for GSE248891
Status Public on Apr 24, 2024
Title ChIP-seq analysis of gene expression regulated by LSD1 in CD8+ T cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ChIP-seq assay was performed with GSK- or Vehicle-treated CD8+ T cells to interrogate the genome-wide distribution of LSD1, H3K4me1, H3K4me2, H3K4me3, H3K27ac, and Pol II, and their alterations in response to LSD1 inhibition.
Overall design In vitro cultured CD8+ T cells were fixed in 1% formaldehyde for 10 min at RT on a shaker, followed by quenching in 125 mM glycine. Next, cells were washed twice with ice-cold PBS and lysed in sonication buffer, then sonicated to obtain DNA fragments mostly between 300-800 bp. Subsequent procedures were performed following the Epigenetics Protocols Database PROT-11 ( ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-01) according to the manufacturer’s instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at Novaseq 6000 (Illumina) to generate 150 bp paired-end reads or at DNBSEQ-T7 (MGI Tech) to generate 100 bp paired-end reads.
Web link http://10.1038/s41467-024-48607-4
Contributor(s) Jiang P, Sheng W
Citation(s) 38773088
Submission date Nov 29, 2023
Last update date May 27, 2024
Contact name Wanqiang Sheng
Organization name Zhejiang University School of Medicine
Department Department of Immunology
Lab The Sheng Lab
Street address 866 Yuhangtang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL28330 DNBSEQ-T7 (Mus musculus)
Samples (16)
GSM7921778 veh_Input1
GSM7921779 veh_LSD1
GSM7921780 veh_H3K4me1
BioProject PRJNA1046394

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Supplementary file Size Download File type/resource
GSE248891_RAW.tar 638.5 Mb (http)(custom) TAR (of BROADPEAK, BW, NARROWPEAK)
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Raw data are available in SRA

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