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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 08, 2024 |
| Title |
H3K27ac Cut&Tag, WT mESCs (EpiLC-1h), Rep1 |
| Sample type |
SRA |
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| Source name |
V65
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| Organism |
Mus musculus |
| Characteristics |
cell line: V65
cell type: mESCs
genotype: WT
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| Growth protocol |
The mESCs stated as EpiLC 0h/2iLif were cultured in 2i/Lif medium, while those stated as EB D0/SL were cultured in Serum/Lif medium.ADFNK differentiation medium and N2B27 basal medium were used for EB differentiation and EpiLC differentiation, respectively.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, cells were harvested, counted, and centrifuged for 3 min at 1,000 rpm at room temperature. About 10,000 cells were washed using washing buffer followed by incubation with Concanavalin A beads at room temperature for 10 min. Next, 1 μl primary antibody was incubated with cells on a rotating platform at 4°C overnight. Secondary antibody incubation followed by pA/G-Tn5 incubation were performed on a rotating platform at room temperature each for 1 h. Between each of the above steps, the beads were washed using corresponding buffer. To activate the activity of Tn5, the beads were incubated in Tagmentation buffer at 37°C for 1 h followed by stop tagmentation using EDTA and extract DNA using DNA clean beads.
Cut&Tag libraries preparation using Hyperactive universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For the bioinformatics analysis, the adapters were cut by Trimmomatic. The data were aligned to mouse genome sequence (mm10) using Bowtie2 with options: –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700 . Samtools was used to remove duplication from bam files. The bigWig files were generated by bamCoverage using CPM as normalization method to show IGV examples . The differential peaks between samples were called using Macs2 with default parameters. ComputerMatrix was used to calculate the peak signals around poised-specific genes from bigWig file normalized by CPM, and the results were visualized by plotHeatmap. The read counts in each peak were extracted using bedtools .
Assembly: mm10
Supplementary files format and content: The bigWig files normalized by CPM of each sample were provided to visualize in IGV or UCSC genome browser.
Library strategy: Cut&Tag
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| Submission date |
Feb 20, 2024 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Xuehui Lv |
| E-mail(s) |
lvxuehui0118@pku.edu.cn
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| Organization name |
Peking University
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| Street address |
No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE256183 |
A DGCR8/FLII-dominated on-off switch for immediate-early genes governs embryo implantation in mouse and human [Cut&Tag] |
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| Relations |
| BioSample |
SAMN40001152 |
| SRA |
SRX23671292 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8087183_CutTag_Rep1_H3K27ac_EpiLC_1h_WT.bw |
70.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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