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Sample GSM8079995 Query DataSets for GSM8079995
Status Public on Feb 19, 2024
Title B16F10 cells, shMi-2β-1
Sample type SRA
 
Source name B16F12
Organism Mus musculus
Characteristics cell line: B16F12
cell type: Mouse melanoma cells
genotype: Mi-2beta knock down
Growth protocol B16F10 cells and primary mouse melanoma cells (extracted and saved by our laboratory) cell were cultured in complete DMEM media (10% FBS and 100U/ml of Penicillin-Streptomycin).
Extracted molecule genomic DNA
Extraction protocol 5 × 104 cells were resuspended in ice-cold nucleus lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and centrifuged at 500 × g for 10 min at 4 °C. The supernatant was discarded, and the transposition reaction was performed using the Tn5 transposase at 37 °C for 30 min.
DNA was purified using a MinElute PCR Purification Kit (Qiagen, Redwood, CA, USA), and the resulting DNA was PCR amplified. The selection of size and purification of DNA fragments were done using the AMPure beads. Size distribution and molarity of the sequencing library were determined by Qubit (Thermo Fisher Scientific, Beverly, MA). Samples were performed in replicates and sequenced on an Illumina PE150 (Illumina) platform. Reads were mapped to the mm10 reference genome
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Samples were performed in replicates and sequenced on an Illumina PE150 (Illumina) platform. Reads were mapped to the mm10 reference genome. Peaks with log2 (fold change) ≥ 0.5 and a P value ≤ 0.05 in comparisons were termed significant. Genome coverage (bedgraph) files were generated by the makeTagdirectory with checkGC parameter, and were used for visualization with IGV2. Read distribution (RD) plots were visualized by the Java TreeView, and histograms were visualized by the GraphPad Prism 5 software (GraphPad Software Inc., San Diego, CA).
Assembly: mm10
Supplementary files format and content: narrow peak
 
Submission date Feb 14, 2024
Last update date Feb 19, 2024
Contact name Zhixiang Xu
E-mail(s) zhixiangxu08@gmail.com
Phone +8613270538760
Organization name 河南大学
Street address Jin Ming Avenue north section
City kaifeng
ZIP/Postal code 475004
Country China
 
Platform ID GPL24247
Series (1)
GSE255782 Mi-2β promotes immune evasion in melanoma by activating EZH2 methylation
Relations
BioSample SAMN39943844
SRA SRX23620867

Supplementary file Size Download File type/resource
GSM8079995_CH-1_peaks.narrowPeak.gz 1.4 Mb (ftp)(http) NARROWPEAK
GSM8079995_CH-1_treat_pileup.bw 647.8 Mb (ftp)(http) BW
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