|
| Status |
Public on Nov 28, 2024 |
| Title |
EedKO_H3K27me3 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Intestine
cell type: Epithelial
genotype: Eed fl/fl Villin-CreER-T2
treatment: Tamoxifen
antibody: H3K27me3
|
| Treatment protocol |
Mouse intestine was dissected and cut into 1cm pieces and treated with 5mM EDTA for 30 minutes with vigurous shaking. Villi were isolated by using 70um filter. Villi were treated by 4X TrypLE to generate single cell suspension.
|
| Growth protocol |
Mouse intestinal epithelial cell.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies, H3K27me3 and H3K4me3 were incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were aligned to GRCm38/mm10 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Samtools version 1.17
Tracks for libraries were generated by converting bam files to to BigWig by deeptools for display on the UCSC browser.
Assembly: GRCm38
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Jan 19, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Unmesh Jadhav |
| E-mail(s) |
[email protected]
|
| Phone |
323-442-2563
|
| Organization name |
University of Southern California
|
| Department |
Stem Cell and Regenerative Medicine
|
| Lab |
Jadhav Lab
|
| Street address |
1425 San Pablo Street
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE253736 |
Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis |
|
| Relations |
| BioSample |
SAMN39510171 |
| SRA |
SRX23330982 |
