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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 19, 2024 |
| Title |
B16F10 cells, shNC-2 |
| Sample type |
SRA |
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| Source name |
B16F11
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| Organism |
Mus musculus |
| Characteristics |
cell line: B16F11
cell type: Mouse melanoma cells
genotype: control
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| 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).
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| 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
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Feb 14, 2024 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Zhixiang Xu |
| E-mail(s) |
zhixiangxu08@gmail.com
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| Phone |
+8613270538760
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| Organization name |
河南大学
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| Street address |
Jin Ming Avenue north section
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| City |
kaifeng |
| ZIP/Postal code |
475004 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE255782 |
Mi-2β promotes immune evasion in melanoma by activating EZH2 methylation |
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| Relations |
| BioSample |
SAMN39943845 |
| SRA |
SRX23620866 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8079994_shNC-2_peaks.narrowPeak.gz |
1.0 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM8079994_shNC-2_treat_pileup.bw |
311.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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